AEGeAn CanonGFF3 |
pre-process GFF3 files, removing all features not directly related to protein-coding genes |
Genome annotation
|
1 |
Genome2Genes |
for genome plots. |
|
1 |
Genome2genes |
Parse a genbank format genome sequences into genes and ammino seqs. |
|
1 |
'FeatureStein' fragment overlay scoring |
feature overlay scoring |
|
1 |
1Dto2D |
Transform 1D tables into 2D array(Tables seperted by \n\n) |
|
1 |
2aliyun |
send files to aliyun server |
|
1 |
2D Feature Extraction |
Feature Extraction |
|
3 |
2Dto1D |
Transform 2D tables into 1D array(Tables seperted by \n\n) |
|
1 |
2DtoArrays |
transform 2D dataframe to Arrays(mxd format) |
|
1 |
A) Format Data for LEfSe |
|
|
1 |
AA Genotype Caller: |
Demultiplex AmpliSeq AccessArray reads and call genotypes for target SNVs |
|
1 |
aaChanges |
amino-acid changes caused by a set of SNPs |
|
2 |
ABRicate |
Mass screening of contigs for antimicrobial and virulence genes |
Antimicrobial resistance prediction
|
9 |
ABRicate List |
List all of abricate's available databases. |
Antimicrobial resistance prediction
|
9 |
ABRicate Summary |
Combine ABRicate results into a simple matrix of gene presence/absence |
Antimicrobial resistance prediction
|
1 |
Abundance index |
computation across species, sites and years |
|
1 |
Abundance index |
computation across species, sites and years |
|
1 |
ABySS |
de novo sequence assembler |
|
9 |
Adapt an elastic transformation |
to a new image size with bUnwarpJ |
|
2 |
Add column |
to an existing dataset |
Editing
|
2 |
Add hydrogen atoms |
at a certain pH value |
|
1 |
Add hydrogen atoms |
at a certain pH value |
|
6 |
Add input name as column |
to an existing tabular file |
|
3 |
Add line to file |
writes a line of text at the begining or end of a text file. |
|
1 |
Add LoFreq alignment quality scores |
to aligned read SAM/BAM records |
|
4 |
Add metadata |
to a BIOM table |
Conversion
Format validation
|
8 |
Add or remove noise |
|
|
2 |
Add or Replace Groups |
|
|
3 |
Add shadow effect |
|
|
2 |
add-read-counts |
Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file |
|
2 |
Add_annotation |
of a fasta sequence |
|
1 |
Add_Colors |
of a fasta sequence |
|
1 |
Add_Tag |
to a dataframe |
|
1 |
AddCommentsToBam |
add comments to BAM dataset |
|
14 |
Adding New Topology Information |
to a GROMACS topology file |
|
1 |
AddOrReplaceReadGroups |
add or replaces read group information |
|
14 |
AddTaxa2Seq |
based on the classification |
|
1 |
Adjust threshold |
of binary image |
|
2 |
Adjust_Oritention |
of DNA sequences |
|
1 |
Admixture |
: Map genomic intervals resembling specified source populations |
|
4 |
Advanced Grep |
|
|
1 |
Advanced NG-CHM Generator |
Create Clustered Heat Maps with Advanced Options |
|
4 |
Advanced restitution: 'Point fixe' protocol |
from Animal Detection on Acoustic Recordings |
|
1 |
Advanced restitution: 'Routier'or 'Pedestre' protocols |
from Animal Detection on Acoustic Recordings |
|
1 |
Advanced restitution: raw approach |
from Animal Detection on Acoustic Recordings |
|
1 |
Advanced restitution: summary |
from Animal Detection on Acoustic Recordings |
|
1 |
AEGeAn GAEVAL |
compute coverage and integrity scores for gene models using transcript alignments. |
Genome annotation
|
1 |
AEGeAn LocusPocus |
calculate locus coordinates for the given gene annotation |
Genome annotation
|
1 |
AEGeAn ParsEval |
compare two sets of gene annotations for the same sequence. |
Genome annotation
|
1 |
Aggregate and filter alignment metrics |
of individual clusters, like the output of graphclust_align_cluster |
|
1 |
Aggregate datapoints |
Appends the average, min, max of datapoints per interval |
|
2 |
Aggregate Individuals |
: Append summary columns for a population |
|
3 |
Aggregator |
Aggregates IsoEM2 output files and generates PCA plots |
|
1 |
Alchemical Analysis |
Analysis of alchemical free energy calculations |
|
1 |
Alevin |
Quantification and analysis of 3-prime tagged-end single-cell sequencing data |
|
8 |
Align GraphClust cluster |
structural alignment and conservation analysis of predicted clusters |
|
1 |
Align reads and estimate abundance |
on a de novo assembly of RNA-Seq data |
|
1 |
Align reads and estimate abundance |
on a de novo assembly of RNA-Seq data |
|
12 |
Align Samples |
- Align peaks across Peaklists |
|
2 |
Align sequences |
to a reference using a codon alignment algorithm |
|
6 |
Align two images |
with bUnwarpJ |
|
2 |
Align.check |
Calculate the number of potentially misaligned bases |
|
6 |
Align.seqs |
Align sequences to a template alignment |
|
5 |
AlignColums |
align 2 tables into 1 tables according to key |
|
1 |
Alignment Extractor: |
Generate reduced reference and bam files to visualize reads in IGV |
|
1 |
Alignment_mapping |
using SOAP1 |
|
1 |
Alignment_mapping |
using SOAP2 |
|
1 |
Alignment_of_16S |
rRNA genes using mothur |
|
1 |
alignmentsieve |
Filter BAM/CRAM files according to specified parameters |
|
7 |
AlignQual |
measurement of quality of bidirectional sequences based on multiple alignments. |
|
1 |
AlignTable |
OTU report according to sequence numbers |
|
1 |
alimask |
append modelmask line to a multiple sequence alignments |
|
7 |
Alleyoop |
- post-processing and QC of Slamdunk analyses |
|
5 |
ALLPATHS-LG |
- assembly of S. aureus and R. sphaeroides datasets |
|
1 |
Alpha Diversity |
of each sample |
|
1 |
Alphafold 2 |
- AI-guided 3D structural prediction of proteins |
Protein structure prediction
|
8 |
Amova |
Analysis of molecular variance |
|
5 |
AmpliCan |
analysis tool for genome editing |
|
1 |
Analyse canonical genes against 'peak' data |
using RnaChipIntegrator |
|
3 |
Analyse CpGo/e ratios |
|
|
1 |
Analyze Covariates |
- draw plots |
|
1 |
Analyze particles |
of binary image |
|
2 |
Analyze skeleton |
|
|
2 |
Ancestry |
: Characterize ancestries w.r.t. inferred ancestral populations |
|
2 |
Angle Analysis |
- time series of Angles |
|
5 |
Anisotropic Diffusion |
Edge-preserving, Anisotropic diffusion |
|
2 |
AnnData Operations |
modifies metadata and flags genes |
|
13 |
Annotate |
a VCF dataset with custom filters |
|
1 |
Annotate |
a VCF file (dbSNP, hapmap) |
|
1 |
Annotate |
a newick tree with HyPhy |
|
6 |
Annotate |
opens an IFrame to Apollo |
|
8 |
Annotate Amplicons |
|
|
1 |
Annotate DESeq2/DEXSeq output tables |
Append annotation from GTF to differential expression tool outputs |
|
2 |
Annotate RNAz |
|
|
1 |
Annotate with DGI |
database info |
|
1 |
annotateMyIDs |
annotate a generic set of identifiers |
|
11 |
annotatePeaks |
|
|
4 |
Annotates |
the depth & breadth of coverage of features from multiple files |
|
1 |
Annotation |
genes based on blastp analysis |
|
1 |
ANNOVAR |
Annotate a file using ANNOVAR |
|
1 |
Anosim |
Non-parametric multivariate analysis of changes in community structure |
|
5 |
ANOSIM |
of a taxonomic OTU reporter to analyze significant difference between treatments;基于OTUreporter或距离矩阵分析不同组之间的差异 |
|
1 |
Anova |
N-way anova. With ou Without interactions |
|
3 |
AnteChamber |
- Amber's molecular input file processor |
|
8 |
antigenic |
Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. |
|
5 |
Antismash |
allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters |
|
7 |
APoc |
Large-scale identification of similar protein pockets |
|
2 |
APOSTL Interactive Analysis |
|
|
1 |
APOSTL Static Bubblegraph Generator |
|
|
1 |
Apply elastic transformation |
with bUnwarpJ |
|
2 |
Apply raw transformation |
with bUnwarpJ |
|
2 |
Apply Variant Recalibration |
|
|
3 |
Apply Variant Recalibration |
|
|
1 |
Arithmetic Operations |
on tables |
|
2 |
Array_vs_NGS |
Compare Genotypes from SNP-array and NGS experiments |
|
1 |
ARTIC guppyplex |
Filter Nanopore reads by read length and (optionally) quality |
|
3 |
ARTIC minion |
Build consensus sequence and call variants from amplicon-based nanopore sequence data |
|
5 |
ASCA |
Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block |
|
1 |
AskoR DE |
EdgeR for AskOmics |
|
1 |
Assemble with MIRA v3.4 |
Takes Sanger, Roche, Illumina, and Ion Torrent data |
|
2 |
AssemblyPostProcessor |
post-processes de novo transcriptome assembly |
|
1 |
Assign Seqs into samples(Updated and slightly tolerant to more errors by beginners) |
assign Seqs into Sampels based on primer and barcode sequences. |
|
1 |
Assign the taxa |
into its parent's taxrank using NCBITAX. |
|
1 |
Assign weighted-average |
of the values of features overlapping an interval |
|
2 |
AssignBarcode |
transform 2D dataframe to Arrays(mxd format) |
|
1 |
AssignSamp2Roots |
assign samples to its coordination according to log and samle name. |
|
1 |
Associate |
HUMAnN2 functions with metadata |
|
3 |
Association of points |
in consecutive frames (slices) using the nearest neighbor algorithm |
|
3 |
Augustus |
gene prediction for prokaryotic and eukaryotic genomes |
|
8 |
Auto Threshold |
applies a standard threshold algorithm to an image |
|
3 |
Autocorrelation test |
check for temporal autocorrelation in the residuals |
|
1 |
Autocorrelation test |
check for temporal autocorrelation in the residuals |
|
1 |
Automated multiple sequence |
alignment with pipelign |
|
1 |
AutoSample |
group samples based on their characteristics(sep by ",". |
|
1 |
AXT to concatenated FASTA |
Converts an AXT formatted file to a concatenated FASTA alignment |
Conversion
|
1 |
AXT to FASTA |
Converts an AXT formatted file to FASTA format |
Conversion
|
1 |
AXT to LAV |
Converts an AXT formatted file to LAV format |
Conversion
|
1 |
B) LDA Effect Size (LEfSe) |
|
|
1 |
backtranseq |
Back translate a protein sequence |
|
7 |
BAFsegment Analysis |
Mosaic CNVs detection on BeadArray data |
|
1 |
Ballgown |
Flexible, isoform-level differential expression analysis |
|
1 |
BAM Coverage Plotter |
Plot read coverage across a genomic contig |
|
1 |
BAM filter |
Removes reads from a BAM file based on criteria |
|
4 |
BAM Index Statistics |
|
|
3 |
BAM to BigWig |
Calculates coverage from a BAM alignment file |
|
3 |
BAM to Wiggle |
converts all types of RNA-seq data from .bam to .wig |
|
10 |
bam-to-bai |
converter |
|
1 |
BAM-to-SAM |
convert BAM to SAM |
|
5 |
BAM/SAM Mapping Stats |
reads mapping statistics for a provided BAM or SAM file. |
|
10 |
bamCompare |
normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them |
|
16 |
bamCoverage |
generates a coverage bigWig file from a given BAM or CRAM file |
|
18 |
BamHash |
Hash BAM and FASTQ files to verify data integrity |
|
1 |
BamLeftAlign |
indels in BAM datasets |
|
12 |
bamPEFragmentSize |
Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files |
|
16 |
BamUtil clipOverlap |
|
Sequence cutting
|
1 |
BamUtil diff |
two coordinate sorted SAM/BAM files |
Sequence cutting
|
1 |
banana |
Bending and curvature plot in B-DNA |
|
5 |
Bandage Image |
visualize de novo assembly graphs |
|
8 |
Bandage Info |
determine statistics of de novo assembly graphs |
|
6 |
bank_inhouse |
search by accurate mass (and by Retention time) on a local bank |
|
1 |
Bar chart |
for multiple columns |
|
2 |
Barcode Splitter |
|
|
4 |
BARIC Expression measure |
|
|
1 |
BARIC Quality of transcriptome assembly |
|
|
1 |
Barplot |
of mean+sd tables. |
|
1 |
Barplot |
stratified HUMAnN features |
Nucleic acid sequence analysis
Phylogenetic analysis
|
3 |
Barplot |
stratified HUMAnN2 features |
|
3 |
barrnap |
Locate ribosomal RNA's in a fasta file. (GFF output) |
|
4 |
BarSplitter |
|
|
1 |
Base Coverage |
of all intervals |
Quantification
|
5 |
Base Recalibrator |
calculates covariates used to recalibrate base quality scores of reads |
|
3 |
Basespace |
getting data |
|
1 |
Basic_Summary |
of a taxonomic OTU reporters |
|
1 |
basil |
Breakpoint detection, including large insertions |
|
1 |
Batch_correction |
Corrects intensities for signal drift and batch-effects |
|
4 |
BaTS |
calculate significance between treatments based on phylogenetic relationships |
|
1 |
bax2bam |
converts PacBio basecall format (bax.h5) into BAM |
Conversion
|
2 |
BayeScan |
Detecting natural selection from population-based genetic data |
|
1 |
BBRIC Faire-Seq analysis |
Analyzing FAIRE-Seq data with MACS2 and deeptools |
|
1 |
BBTools: BBduk |
decontamination using kmers |
Global alignment
Pairwise sequence alignment
|
3 |
BBTools: BBMap |
short-read aligner |
|
4 |
BBTools: call variants |
in aligned Bam files |
|
2 |
BCF Tools Cat |
This tool allows the user to concatenate BCF files. |
|
2 |
BCF Tools Index |
This tool allows the user to index sorted BCF for random access. |
|
2 |
bcf_uncompressed-to-bcf |
converter |
|
1 |
bcftools annotate |
Annotate and edit VCF/BCF files |
|
11 |
bcftools call |
SNP/indel variant calling from VCF/BCF |
|
12 |
bcftools cnv |
Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values |
|
14 |
bcftools color-chrs |
plugin Color shared chromosomal segments, requires phased GTs |
|
8 |
bcftools concat |
Concatenate or combine VCF/BCF files |
|
10 |
bcftools consensus |
Create consensus sequence by applying VCF variants to a reference fasta file |
|
13 |
bcftools convert from vcf |
Converts VCF/BCF to IMPUTE2/SHAPEIT formats |
|
10 |
bcftools convert to vcf |
Converts other formats to VCF/BCFk |
|
10 |
bcftools counts |
plugin counts number of samples, SNPs, INDELs, MNPs and total sites |
|
11 |
bcftools csq |
Haplotype aware consequence predictor |
|
11 |
bcftools dosage |
plugin genotype dosage |
|
10 |
bcftools fill-AN-AC |
plugin Fill INFO fields AN and AC |
|
10 |
bcftools fill-tags |
plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi |
|
10 |
bcftools filter |
Apply fixed-threshold filters |
|
10 |
bcftools fixploidy |
plugin Fix ploidy |
|
10 |
bcftools frameshifts |
plugin Annotate frameshift indels |
|
8 |
bcftools gtcheck |
Check sample identity |
|
10 |
bcftools impute-info |
plugin Add imputation information metrics to the INFO field |
|
10 |
bcftools isec |
Create intersections, unions and complements of VCF files |
|
11 |
bcftools List Samples |
in VCF/BCF file |
|
10 |
bcftools mendelian |
plugin Count Mendelian consistent / inconsistent genotypes |
|
10 |
bcftools merge |
Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file |
|
11 |
bcftools missing2ref |
plugin Set missing genotypes |
|
10 |
bcftools mpileup |
Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files |
|
11 |
bcftools norm |
Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows |
|
13 |
bcftools query |
Extracts fields from VCF/BCF file and prints them in user-defined format |
|
11 |
bcftools reheader |
Modify header of VCF/BCF files, change sample names |
|
10 |
bcftools roh |
HMM model for detecting runs of homo/autozygosity |
|
10 |
bcftools setGT |
plugin Sets genotypes |
|
10 |
bcftools stats |
Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats |
|
12 |
bcftools tag2tag |
plugin Convert between similar tags, such as GL and GP |
|
12 |
bcftools view |
VCF/BCF conversion, view, subset and filter VCF/BCF files |
|
14 |
Beagle |
phasing genotypes and imputing ungenotyped markers |
Haplotype mapping
|
1 |
BEAM |
significant single- and multi-locus SNP associations in case-control studies |
|
1 |
bed to protein map |
genomic location of proteins for MVP |
|
2 |
BED-to-bigBed |
converter |
Conversion
|
2 |
BED-to-GFF |
converter |
|
2 |
BED-to-GFF |
converter |
Conversion
|
1 |
bed_clean |
clean up BED files |
|
1 |
bed_closest |
find closest intervals |
|
1 |
bed_collapse |
collapse intervals |
|
1 |
bed_intersect |
intersect two interval sets |
|
1 |
bed_overlap_significance |
significance of two interval sets overlapping |
|
1 |
bed_resize |
change interval size |
|
1 |
bed_shuffle |
shuffle intervals chromosome not weighted by length |
|
1 |
bed_size_stat |
plot interval size distribution |
|
1 |
bed_sort_with_header |
sort intervals with header lines |
|
1 |
bed_to_bigwig |
make bigwig from BED or BAM |
|
1 |
bed_window |
make a window around interval center |
|
1 |
BedCov |
calculate read depth for a set of genomic intervals |
|
5 |
bedgraph-to-bigwig |
converter |
|
1 |
BedToIntervalList |
convert coordinate data into picard interval list format |
|
14 |
bedtools AnnotateBed |
annotate coverage of features from multiple files |
|
21 |
bedtools BAM to BED |
converter |
|
23 |
bedtools BED to BAM |
converter |
|
21 |
bedtools BED to IGV |
create batch script for taking IGV screenshots |
|
16 |
bedtools BED12 to BED6 |
converter |
|
20 |
bedtools BEDPE to BAM |
converter |
|
21 |
bedtools ClosestBed |
find the closest, potentially non-overlapping interval |
|
21 |
bedtools ClusterBed |
cluster overlapping/nearby intervals |
|
20 |
bedtools ComplementBed |
Extract intervals not represented by an interval file |
|
21 |
bedtools ExpandBed |
replicate lines based on lists of values in columns |
|
20 |
bedtools FisherBed |
calculate Fisher statistic between two feature files |
|
20 |
bedtools FlankBed |
create new intervals from the flanks of existing intervals |
|
21 |
bedtools Genome Coverage |
compute the coverage over an entire genome |
|
20 |
bedtools GroupByBed |
group by common cols and summarize other cols |
|
20 |
bedtools JaccardBed |
calculate the distribution of relative distances between two files |
|
20 |
bedtools LinksBed |
create a HTML page of links to UCSC locations |
|
20 |
bedtools MakeWindowsBed |
make interval windows across a genome |
|
21 |
bedtools MaskFastaBed |
use intervals to mask sequences from a FASTA file |
|
20 |
bedtools Merge BedGraph files |
combines coverage intervals from multiple BEDGRAPH files |
|
20 |
bedtools MergeBED |
combine overlapping/nearby intervals into a single interval |
|
20 |
bedtools MultiCovBed |
counts coverage from multiple BAMs at specific intervals |
|
20 |
bedtools Multiple Intersect |
identifies common intervals among multiple interval files |
|
23 |
bedtools OverlapBed |
computes the amount of overlap from two intervals |
|
20 |
bedtools RandomBed |
generate random intervals in a genome |
|
21 |
bedtools ReldistBed |
calculate the distribution of relative distances |
|
20 |
bedtools ShuffleBed |
randomly redistrubute intervals in a genome |
|
21 |
bedtools SlopBed |
adjust the size of intervals |
|
22 |
bedtools SortBED |
order the intervals |
|
20 |
bedtools SpacingBed |
reports the distances between features |
|
17 |
bedtools SubtractBed |
remove intervals based on overlaps |
|
20 |
bedtools TagBed |
tag BAM alignments based on overlaps with interval files |
|
20 |
bedtools WindowBed |
find overlapping intervals within a window around an interval |
|
20 |
Beta Diversity |
using scikit-bio |
|
1 |
Between-table Correlation |
Correlation table between two tables and graphic representation |
|
2 |
BiDataframeCompare |
compare two dataframe. |
|
1 |
BigWig to Wig |
converter |
|
1 |
bigwig-to-wig |
converter |
|
1 |
bigwigCompare |
normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them |
|
16 |
bigWigToBedGraph |
Convert from bigWig to bedGraph format |
|
2 |
bim_input |
prepare BIM input |
|
1 |
Bin.seqs |
Order Sequences by OTU |
|
5 |
Binary 2 Label |
Converts Binary to Label Image |
|
2 |
Binary To Points |
Converts Binary Image to Points |
|
1 |
Binning refiner |
refines metagenome bins |
|
2 |
Bio-TraDis counts to gene insertion data |
|
|
1 |
Bio-TraDis Essentiality Predictions |
|
|
1 |
Bio-TraDis reads to counts |
|
|
1 |
BioInfoMiner |
Interpretation of -omic data |
|
1 |
Biom.info |
create shared and taxonomy files from biom |
|
2 |
biom2-to-biom1 |
converter |
|
1 |
Bionano Hybrid Scaffold |
automates the scaffolding process |
Genome assembly
|
7 |
biosed |
Replace or delete sequence sections |
|
5 |
Biosigner |
Molecular signature discovery from omics data |
|
2 |
biosyntheticSPAdes |
biosynthetic gene cluster assembly |
|
6 |
Bismark Deduplicate |
Deduplicates reads mapped by Bismark |
|
9 |
Bismark Mapper |
Bisulfite reads mapper |
|
15 |
Bismark Meth. Extractor |
Reports on methylation status of reads mapped by Bismark |
|
11 |
Bismark Pretty Report |
Generates a graphical HTML report page from report outputs of Bismark |
|
9 |
Blank Filter |
- Remove 'blank' peaks from the biological mass spectra |
|
2 |
BLAST |
analysis (Standalone) . |
|
1 |
BLAST |
analyses locally |
|
1 |
BLAST parser |
Convert 12- or 24-column BLAST output into 3-column hcluster_sg input |
|
2 |
BLAST Reciprocal Best Hits (RBH) |
from two FASTA files |
|
5 |
BLAST top hit descriptions |
Make a table from BLAST output |
|
2 |
BLAST XML to selected tabular columns |
Convert BLAST XML output to tabular |
|
1 |
BLAST XML to tabular |
Convert BLAST XML output to tabular |
Conversion
|
18 |
Blast2GFF |
convert BLAST txt output to GFF |
|
1 |
Blast2GO |
Maps BLAST results to GO annotation terms |
|
3 |
BLASTClassifier |
using lowest common ancestor based on blastp/blastn analysis |
|
1 |
BLASTP2KO2GO |
based on ammino acid sequences of genes |
|
1 |
blastx |
analysis against bacteriaref curated from NCBI |
|
1 |
BLASTXFrame |
get the correct translation frame. |
|
1 |
BlastXML to gapped GFF3 |
|
|
1 |
BLAT |
|
|
1 |
Blat |
BLAT sequence search |
|
1 |
blockbuster |
detects blocks of overlapping reads using a gaussian-distribution approach |
|
3 |
BlockClust |
efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles |
|
2 |
bowtie-to-bed |
converter |
|
1 |
Bowtie2 |
- map reads against reference genome |
|
21 |
Boxplot |
of quality statistics |
|
2 |
Boxplot |
of community composition using different sets of explaining matrixs |
|
1 |
Boxplot(ggplot) |
of dataframes |
|
1 |
Braker genome annotation |
|
|
1 |
BraydistBoxplot |
of a distant matrix |
|
1 |
breakdancer |
detection of structural variants |
|
1 |
breseq |
find mutations in haploid microbial genomes |
DNA mapping
Genetic mapping
Genome annotation
Mapping assembly
Protein SNP mapping
Sequence word comparison
|
4 |
btwisted |
Calculates the twisting in a B-DNA sequence |
|
5 |
Build a GeneNoteBook |
|
|
1 |
Build base quality distribution |
|
|
1 |
Build custom track |
for UCSC genome browser |
|
3 |
Build Deep learning Batch Training Models |
with online data generator for Genomic/Protein sequences and images |
|
5 |
Build expression matrix |
for a de novo assembly of RNA-Seq data by Trinity |
|
1 |
Build expression matrix |
for a de novo assembly of RNA-Seq data by Trinity |
|
12 |
Build tLEaP |
interactively build and run tLEaP files to set up systems with AmberTools |
|
1 |
Busco |
assess genome assembly and annotation completeness |
|
15 |
Butina Cluster |
using RDKit |
|
2 |
Butina Cluster Matrix |
using RDKit |
|
2 |
Butterfly data analysis and graph display |
|
|
1 |
BWA-MEM2 |
- map medium and long reads (> 100 bp) against reference genome |
|
1 |
bwameth |
Fast and accurate aligner of BS-Seq reads. |
|
6 |
C) Plot LEfSe Results |
|
|
1 |
cai |
CAI codon adaptation index |
|
5 |
cai custom |
CAI codon adaptation index using custom codon usage file |
|
5 |
Calculate a Heinz score |
for each node |
|
2 |
Calculate bray curtis |
based on a data frame |
|
1 |
Calculate community metrics |
calculate community metrics from abundance data |
|
3 |
Calculate contig depths |
for MetaBAT2 |
|
3 |
Calculate CpNo/e |
|
|
1 |
Calculate interference |
Tool for calculating possible background interference for a set of target peptides |
|
1 |
Calculate metrics |
for classification performance |
|
12 |
Calculate metrics |
for regression performance |
|
11 |
Calculate molecular descriptors |
with Mordred |
|
3 |
Calculate plane of best fit for molecules |
using RDKit |
|
2 |
Calculate presence absence table |
calculate presence absence table from observation data |
|
3 |
Calculate protein properties |
|
|
2 |
Calculate sequence complexity |
total and per read |
|
3 |
Calculate the box parameters using RDKit |
for an AutoDock Vina job from a ligand or pocket input file (confounding box) |
|
5 |
calculate_aa_freqs |
calculate aminoacid frequencies |
|
1 |
Calculate_Pairwise |
distance between DNA sequences. |
|
1 |
Call and phase |
heterozygous SNPs |
|
4 |
Call CNVs |
|
|
1 |
Call specific mutations in reads: |
Looks for reads with mutation at known positions and calculates frequencies and stats. |
|
3 |
Call variants |
with LoFreq |
|
7 |
CAMERA.annotate |
CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. |
|
9 |
CAMERA.combinexsAnnos |
Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. |
|
9 |
Canonical Correlation Analysis |
|
|
1 |
Canu assembler |
Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore |
|
4 |
CarthaGene |
is a genetic/radiated hybrid mapping software. |
|
1 |
cast |
expand combinations of variables:values to columnar format |
|
1 |
CAT add_names |
annotate with taxonomic names |
|
1 |
CAT bins |
annotate with taxonomic classification |
|
2 |
CAT contigs |
annotate with taxonomic classification |
|
2 |
CAT prepare |
a database for CAT - Contig Annotation Tool |
|
1 |
CAT summarise |
the number of contigs or bins assigned to each taxonomic name |
|
1 |
Categorize by Function |
|
|
1 |
Categorize Elements |
satisfying criteria |
|
1 |
CCAT |
Control-based ChIP-seq Analysis Tool |
|
2 |
CCCP: |
Run Consensus Caller Cross-Platform pipeline |
|
1 |
CD-HIT PROTEIN |
Cluster a protein dataset into representative sequences |
|
3 |
cd-hit-dup |
remove duplicates and detect chimaeras in sequencing reads |
|
1 |
CD-HIT-EST |
Cluster a nucleotide dataset into representative sequences |
|
3 |
CDF |
plot of multiple numeric columns |
|
1 |
CDO get info |
Climate Data Information Operators to get information on Climate and NWP model data |
Calculation
|
1 |
CDO Operations |
Climate Data Manipulation Operators operations for standard processing of climate and NWP model output. |
Calculation
|
1 |
CellProfiler |
run a CellProfiler pipeline |
|
2 |
CEMiTool |
gene co-expression network analyses |
|
1 |
CESM |
Community Earth System Model |
Ecological modelling
Modelling and simulation
|
1 |
Change Case |
of selected columns |
|
2 |
Change Title |
to meta-data value. |
|
1 |
Change title |
to metadata value. |
|
6 |
Changechar |
Replace a character by another one |
|
1 |
chaos |
Create a chaos game representation plot for a sequence |
|
5 |
charge |
Protein charge plot |
|
5 |
Check data frame |
:data frame with different number of elements cause problems in the following analysis. Here we kick off those problematic lines. |
|
1 |
Check Format |
Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files |
|
2 |
Check PE FastQ Sync |
|
|
1 |
Check STR motif compatibility between reference and read STRs |
|
|
1 |
CheckAlignment |
remove undesired region of a multiple sequence alignment. |
|
1 |
CheckBarcode |
If something is wrong with Assign seqs into samples,this tool helps check the barcode pair. you can compare this result and adjust your tag file. |
|
1 |
CheckKEGGModuleBritebyTaxa |
Check summarized KEGG module/brite by Taxa. 根际不同KEGG moudle 和Brite的分析结果。 |
|
1 |
CheckSequences |
of a fasta file |
|
1 |
checktrans |
Reports STOP codons and ORF statistics of a protein |
|
5 |
ChEMBL structure pipeline |
for curation and standardizing of molecular structures |
|
2 |
chicAggregateStatistic |
computes with a target file the to be tested regions for chicDifferentialTest |
|
7 |
chicDifferentialTest |
computes differential interactions of viewpoints |
|
7 |
chicPlotViewpoint |
creates plots for viewpoints |
|
7 |
chicQualityControl |
generates an estimate of the quality of each viewpoint |
|
7 |
chicSignificantInteractions |
computes viewpoints with the given reference points and a background model |
|
7 |
chicViewpoint |
computes viewpoints with the given reference points and a background model. |
|
7 |
chicViewpointBackgroundModel |
compute a background model for cHi-C / HiChIP data |
|
6 |
Chimera.bellerophon |
Find putative chimeras using bellerophon |
|
5 |
Chimera.ccode |
Find putative chimeras using ccode |
|
6 |
Chimera.check |
Find putative chimeras using chimeraCheck |
|
5 |
Chimera.perseus |
Find putative chimeras using chimeraCheck |
|
6 |
Chimera.pintail |
Find putative chimeras using pintail |
|
5 |
Chimera.slayer |
Find putative chimeras using slayer |
|
5 |
Chimera.uchime |
Find putative chimeras using uchime |
|
5 |
Chimera.vsearch |
find potential chimeric sequences using vsearch |
|
4 |
ChIPpeakAnno annoPeaks |
annotate peaks by annoGR object in the given range |
|
1 |
chips |
Codon usage statistics |
|
5 |
ChIPseeker |
for ChIP peak annotation and visualization |
|
6 |
ChiRA collapse |
deduplicate fastq reads |
|
17 |
ChiRA extract |
extrat the chimeras |
|
17 |
ChiRA map |
map reads to trascriptome |
|
17 |
ChiRA merge |
merge aligned positions |
|
17 |
ChiRA qauntify |
quantify aligned loci to score the alignments |
|
17 |
Chop.seqs |
Trim sequences to a specified length |
|
6 |
Chromeister |
ultra-fast pairwise genome comparisons |
|
5 |
CIRCexplorer |
|
|
2 |
Circos |
visualizes data in a circular layout |
Visualisation
|
11 |
Circos Builder |
creates circos plots from standard bioinformatics datatypes. |
|
2 |
Circos: Alignments to links |
reformats alignment files to prepare for Circos |
Parsing
|
10 |
Circos: bigWig to Scatter |
reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots |
Conversion
|
10 |
Circos: Bundle Links |
reduce numbers of links in datasets before plotting |
Aggregation
|
10 |
Circos: Interval to Circos Text Labels |
reformats interval files to prepare for Circos text labels |
Conversion
|
10 |
Circos: Interval to Tiles |
reformats interval files to prepare for Circos tile plots |
Conversion
|
10 |
Circos: Link Density Track |
reduce links to a density plot |
Aggregation
|
10 |
Circos: Resample 1/2D data |
reduce numbers of points in a dataset before plotting |
Aggregation
|
10 |
Circos: Stack bigWigs as Histogram |
reformats for use in Circos stacked histogram plots |
Formatting
|
6 |
Circos: Table viewer |
easily creates circos plots from tabular data |
Visualisation
|
10 |
cirdna |
Draws circular maps of DNA constructs |
|
5 |
Classifier |
of 16S rRNA or other functional gene sequences. |
|
1 |
Classify.otu |
Assign sequences to taxonomy |
|
5 |
Classify.rf |
description |
|
2 |
Classify.seqs |
Assign sequences to taxonomy |
|
5 |
Classify.tree |
Get a consensus taxonomy for each node on a tree |
|
5 |
CleanSam |
perform SAM/BAM grooming |
|
14 |
Clearcut |
Generate a tree using relaxed neighbor joining |
|
5 |
climate stripes |
from timeseries |
Visualisation
|
3 |
ClinVarAnnotator |
Flags variants found in the ClinVar database |
|
1 |
Clip |
adapter sequences |
|
6 |
Clipping Profile |
estimates clipping profile of RNA-seq reads from BAM or SAM file |
|
10 |
CliqueSNV |
is a novel reference-based method for reconstruction of viral variants from NGS data. |
|
1 |
Close relatives |
: Discover familial relationships |
|
2 |
CloudMap: Check snpEff Candidates |
Marks up a snpEff output file with matches to a gene candidate list. |
|
1 |
CloudMap: EMS Variant Density Mapping |
Map a mutation by linkage to regions of high mutation density using WGS data |
|
1 |
CloudMap: Hawaiian Variant Mapping with WGS data |
Map a mutation by plotting recombination frequencies resulting from crossing to a highly polymorphic strain |
|
1 |
CloudMap: in silico complementation |
Perform in silico complementation analysis on multiple tabular snpEff output files |
|
1 |
CloudMap: Variant Discovery Mapping with WGS data |
Map a mutation using in silico bulk segregant linkage analysis using variants that are already present in the mutant strain of interest (rather than those introduced by a cross to a polymorphic strain). |
|
1 |
ClustalW |
multiple sequence alignment program for DNA or proteins |
|
5 |
Cluster |
Assign sequences to OTUs (Operational Taxonomic Unit) |
|
4 |
Cluster |
the intervals of a dataset |
Sequence clustering
Sequence merging
|
5 |
Cluster 3 |
Cluster 3.0 |
|
1 |
Cluster Inspection using RaceID |
examines gene expression within clusters |
|
6 |
Cluster KEGG |
: Group gene categories connected by shared genes |
|
2 |
Cluster ligands using SuCOS |
based on the overlap of 3D features |
|
3 |
Cluster OTU |
Cluster OTUs |
|
1 |
Cluster Profiler Bitr |
converting ID types |
|
1 |
Cluster Profiler GO |
run GO Analysis |
|
1 |
Cluster, infer trajectories and embed |
with scanpy |
|
7 |
Cluster.classic |
Assign sequences to OTUs (Dotur implementation) |
|
5 |
Cluster.fragments |
Group sequences that are part of a larger sequence |
|
5 |
Cluster.split |
Assign sequences to OTUs and split large matrices |
|
5 |
cluster_collection_report |
|
|
4 |
ClusterFast |
|
|
1 |
Clustering using RaceID |
performs clustering, outlier detection, dimensional reduction |
|
6 |
ClustQualify |
annotates clusters according to gff annotation files |
|
1 |
ClustToGFF |
add clusters locations into GFF files to be integrated into a genome viewer |
|
1 |
cmalign |
Align sequences to a covariance model against a sequence database |
|
3 |
cmbuild |
Build covariance models from sequence alignments |
|
4 |
CMCV |
visualization of comparisons between RNA family models (CM) |
|
1 |
cmfinder |
|
|
3 |
CML to InChI |
|
|
2 |
CML to mol2 |
|
|
2 |
CML to SDF |
|
|
2 |
cml-to-mol2 |
converter |
|
1 |
cml-to-smi |
converter |
|
2 |
cmpress |
Prepare a covariance model database for cmscan |
|
2 |
cmscan |
Search sequences against collections of covariance models |
|
2 |
cmsearch |
Search covariance model(s) against a sequence database |
|
3 |
cmstat |
Summary statistics for covariance model |
|
3 |
cmv |
CMV is a tool for visualization of RNA family models, also known as covariance models (CM) |
|
2 |
codcmp |
Codon usage table comparison |
|
5 |
codeML |
Detects positive selection (paml package) |
|
3 |
coderet |
Extract CDS, mRNA and translations from feature tables |
|
5 |
Cofold |
An RNA secondary structure prediction method that takes co-transcriptional folding into account |
|
1 |
Cojac: mutbamscan |
scan an alignment file for mutation co-occurrences |
|
1 |
Cojac: tabmut |
export cooccurrence mutations as a table |
|
1 |
Collapse |
sequences |
|
3 |
Collapse Collection |
into single dataset in order of the collection |
|
5 |
Collect Alignment Summary Metrics |
writes a file containing summary alignment metrics |
|
14 |
Collect.shared |
Generate collector's curves for calculators on OTUs |
|
5 |
Collect.single |
Generate collector's curves for OTUs |
|
6 |
CollectBaseDistributionByCycle |
charts the nucleotide distribution per cycle in a SAM or BAM dataset |
|
14 |
CollectGcBiasMetrics |
charts the GC bias metrics |
|
14 |
CollectHsMetrics |
compute metrics about datasets generated through hybrid-selection (e.g. exome) |
|
4 |
CollectInsertSizeMetrics |
plots distribution of insert sizes |
|
14 |
Collector’s curve |
of sequencing yield over time |
|
2 |
CollectRnaSeqMetrics |
collect metrics about the alignment of RNA to various functional classes of loci in the genome |
|
15 |
CollectWgsMetrics |
compute metrics for evaluating of whole genome sequencing experiments |
|
14 |
Colocalization |
of two segmentation maps |
|
1 |
ColorToGray |
converts color and channel-stacked images to grayscale |
|
2 |
Column arrange |
by header name |
|
2 |
Column Join |
|
|
1 |
Column Join |
on Collections |
|
5 |
Column Regex Find And Replace |
|
|
6 |
combine |
combine test.fa with control.fa into test_control.fa |
|
1 |
Combine FASTA and QUAL |
into FASTQ |
Aggregation
|
5 |
Combine Fasta files |
Combine multiple fasta files into one file |
|
1 |
Combine mapped faux paired-end reads |
and get the reference STR allele from the reference genome |
|
2 |
Combine MetaPhlAn2 and HUMAnN2 outputs |
to relate genus/species abundances and gene families/pathways abundances |
|
3 |
Combine read profile probabilities |
from the same allele combination |
|
1 |
Combine tables |
into a result table. |
|
1 |
Combine Variants |
|
|
3 |
Combine Variants |
|
|
1 |
Combine_Annotation |
of a genome |
|
1 |
Combine_colSums |
of several dataframes into a new datasets |
|
1 |
Combine_Columns |
of data frame |
|
1 |
Combine_Multi_Table |
based on the first columns. |
|
1 |
CombineDifferntTablesBySamples |
Combine multiple tables into a dataframe according to sample names(Only consider samples in all tables). |
|
1 |
CombinePDF |
two pdfs page by page. |
|
1 |
Commet |
COmpare Multiple METagenomes |
|
3 |
CommonFastq |
retrieve common sequence from paired fastq files based on seqid. |
|
1 |
CommonForRev |
for short reads analysis(Get common sequneces based on id or description from paired reads. |
|
1 |
Community compositon comparison |
between different methods using pairwise braycurtis distance. |
|
1 |
CommunityToSpatial |
diffence in community composition vs difference in spatial distance. |
|
1 |
Compalignp |
Fractional identities between alignments |
|
2 |
Compare |
multiple VCF datasets |
|
1 |
Compare elastic and raw deformation |
by warping index with bUnwarpJ |
|
2 |
Compare opposite elastic deformations |
by warping index with bUnwarpJ |
|
2 |
Compare outputs of HUMAnN2 for several samples |
and extract similar and specific information |
|
2 |
Compare two Datasets |
to find common or distinct rows |
Filtering
|
1 |
Compare two raw deformations |
by warping index with bUnwarpJ |
|
2 |
Compare_treatments |
dissimilarity between treatments based on a dist matrix |
|
1 |
CompareOTUreporter |
compare common samples in two OTUreporter. |
|
1 |
Complement |
intervals of a dataset |
Sequence coordinate conversion
|
6 |
Compose a raw and an elastic transformation |
into a raw transformation with bUnwarpJ |
|
2 |
Compose two elastic transformations |
into a raw transformation with bUnwarpJ |
|
2 |
Compose two raw transformations |
into another raw transformation with bUnwarpJ |
|
2 |
Compound conversion |
- interconvert between various chemistry and molecular modeling data files |
|
6 |
Compound Convert |
Converts various chemistry and molecular modeling data files |
|
1 |
Compound Search |
an advanced molecular grep program using SMARTS |
|
1 |
Compound search |
- an advanced molecular search program using SMARTS |
|
5 |
Compress file(s) |
|
|
1 |
compseq |
Count composition of dimer/trimer/etc words in a sequence |
|
5 |
Computation with PWMs |
Computations with PWM |
|
1 |
Compute |
on rows |
|
10 |
Compute both the depth and breadth of coverage |
of features in file B on the features in file A (bedtools coverage) |
|
21 |
Compute contig Ex90N50 statistic and Ex90 transcript count |
from a Trinity assembly |
|
10 |
Compute energy profile |
Compute energy profile |
|
1 |
Compute energy PWM |
Compute energy PWM |
|
1 |
Compute GLM on community data |
Compute a GLM of your choice on community data |
|
2 |
Compute GLM on population data |
Compute a GLM of your choice on population data |
|
2 |
Compute Motif Frequencies |
in indel flanking regions |
|
2 |
Compute Motif Frequencies For All Motifs |
motif by motif |
|
2 |
Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features |
between two datasets using Discrete Wavelet Transfoms |
|
2 |
Compute P-values and Max Variances for Feature Occurrences |
in one dataset using Discrete Wavelet Transfoms |
|
2 |
Compute P-values and Second Moments for Feature Occurrences |
between two datasets using Discrete Wavelet Transfoms |
|
2 |
Compute partial R square |
|
|
1 |
Compute physico-chemical properties |
for a set of molecules |
|
1 |
Compute physico-chemical properties |
for a set of molecules |
|
5 |
Compute quality statistics |
for SOLiD data |
|
1 |
Compute quality statistics |
|
|
3 |
Compute RCVE |
|
|
1 |
Compute sequence length |
|
|
6 |
computeGCBias |
Determine the GC bias of your sequenced reads |
|
17 |
computeMatrix |
prepares data for plotting a heatmap or a profile of given regions |
|
18 |
computeMatrixOperations |
Modify or combine the output of computeMatrix in a variety of ways. |
|
11 |
Concat fastq files |
Concatenates fastq files you select from your history |
|
1 |
Concat fastq files (dev version) |
Concatenates fastq files you select from your history |
|
1 |
Concatenate |
two BED files |
Aggregation
|
6 |
Concatenate |
FASTA alignment by species |
|
3 |
Concatenate datasets |
tail-to-head |
Aggregation
|
1 |
Concatenate datasets |
tail-to-head (cat) |
|
11 |
Concatenate images |
|
|
2 |
Concatenate multiple datasets |
tail-to-head |
|
1 |
Concatenate multiple datasets |
tail-to-head |
|
1 |
CONCOCT |
for metagenome binning |
|
4 |
CONCOCT: Cut up contigs |
in non-overlapping or overlapping parts of equal length |
|
4 |
CONCOCT: Extract a fasta file |
for each cluster |
|
4 |
CONCOCT: Generate the input coverage table |
for CONCOCT |
|
4 |
CONCOCT: Merge cut clusters |
and assign concensus clusters for the original contigs |
|
4 |
Condense |
consecutive characters |
|
2 |
Conformer calculation |
for molecules (confab) with OpenBabel |
|
3 |
Connect to Genbank |
|
|
1 |
Consensus.seqs |
Find a consensus sequence for each OTU or phylotype |
|
6 |
Constrained conformer generation |
with RDKit |
|
2 |
Construct Expression Set Object |
Create an ExpressionSet object from tabular and textual data |
|
5 |
Control-FREEC |
detects copy-number changes and allelic imbalances |
|
3 |
Conversion GCMS PostRun Analysis to IsoCor |
|
|
1 |
Convert |
delimiters to TAB |
|
1 |
Convert |
SOLiD output to fastq |
|
1 |
Convert |
KEGG identifier to outside identifier or vice versa |
|
1 |
Convert |
between BIOM table formats |
|
9 |
Convert |
: CSV, FSTAT, Genepop or VCF to either gd_snp or gd_genotype |
|
2 |
Convert a 10X BAM file to FASTQ |
|
|
1 |
Convert Amber topology and coordinate files to GROMACS format |
using acpype |
|
1 |
Convert BAM |
to FASTA multiple sequence alignment |
|
5 |
convert BAM to FASTA/Q |
|
|
1 |
Convert BAM to ScIdx |
|
|
2 |
Convert BCF to BCF_BGZIP |
|
|
1 |
Convert BCF to uncompressed BCF |
|
|
1 |
Convert BCF_BGZIP to BCF |
|
|
1 |
Convert BED to Feature Location Index |
|
|
1 |
Convert BED to GFF |
|
|
2 |
Convert binary image to EDM |
(Euclidean Distance Map) |
|
2 |
Convert Biom1 to Biom2 |
|
|
1 |
Convert Biom2 to Biom1 |
|
|
1 |
Convert DIMSpy-based HDF5 to tsv |
|
|
2 |
Convert elastic transformation to raw |
with bUnwarpJ |
|
2 |
Convert FASTA to 2bit |
|
|
2 |
Convert FASTA to Bowtie base space Index |
|
|
2 |
Convert FASTA to Bowtie color space Index |
|
|
2 |
Convert FASTA to len file |
|
|
2 |
Convert FASTA to Tabular |
|
|
1 |
Convert FeelNC GTF |
to GFF3 for AskOmics |
|
1 |
Convert from BAM to FastQ |
|
|
13 |
Convert genome coordinates |
between assemblies and genomes |
|
2 |
Convert Genomic Intervals To BED |
|
|
1 |
Convert Genomic Intervals To Coverage |
|
|
2 |
Convert Genomic Intervals To Strict BED |
|
|
2 |
Convert Genomic Intervals To Strict BED12 |
|
|
1 |
Convert Genomic Intervals To Strict BED6 |
|
|
2 |
Convert GFF to BED |
|
|
2 |
Convert GFF to Feature Location Index |
|
|
1 |
Convert GFF3 |
to prot_table for TRANSIT |
|
4 |
Convert gffCompare annotated GTF to BED |
for StringTie results |
|
4 |
Convert Glimmer to GFF |
|
|
1 |
Convert GTF to BED12 |
|
|
1 |
Convert image |
Convert image |
|
2 |
Convert informative read depth to sequencing depth |
for flank-based mapping of microsatellites |
|
1 |
Convert Kraken |
data to Galaxy taxonomy representation |
|
3 |
Convert Len file to Linecount |
|
|
2 |
Convert lped to fped |
|
|
2 |
Convert lped to plink pbed |
|
|
2 |
Convert MAF to Fasta |
|
|
2 |
Convert MAF to Genomic Intervals |
|
|
2 |
Convert miRanda output to tabular |
for AskOmics |
|
1 |
Convert Parameters |
to AMBER prmtop in preparation for MMGBSA/MMPBSA |
|
7 |
Convert Picard Interval List to BED6 |
converter |
|
2 |
Convert plink pbed to ld reduced format |
|
|
2 |
Convert plink pbed to linkage lped |
|
|
2 |
Convert SAM |
to interval |
|
2 |
Convert SAM to BAM |
|
|
1 |
Convert to binary |
(black and white) |
|
2 |
Convert VCF to MAF |
with vcf2maf |
|
3 |
Convert XMFA to gapped GFF3 |
|
|
3 |
Convert, Merge, Randomize |
BAM datasets and perform other transformations |
|
7 |
ConvertFastaToPrositCSV |
Create Prosit CSV Input From a Protein FASTA |
|
3 |
Converting multiple OpenLabCDS Text Files to a CSV summary file |
|
|
1 |
ConvertLibraryToBlib |
Convert EncyclopeDIA Library to BLIB for Skyline |
|
3 |
ConvertObjectsToImage |
convert the identified objects into an image |
|
2 |
ConvertPrositCSVToLibrary |
Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library |
|
3 |
Converts GTF to Annotations file for Homer |
|
|
1 |
Converts RDF/XML to other formats |
Converts RDF/XML to one of RDF/XML-ABBREV, N3, N-TRIPLE, TURTLE or tabular |
|
1 |
CoNvex |
Gap-cost alignMents for Long Reads |
|
2 |
Cooccurrence |
tests whether presence-absence patterns differ from chance |
|
6 |
Coocurrence Network |
based on OTU reporter. |
|
1 |
cooler csort with tabix |
Sort and index a contact list. |
|
1 |
cooler_balance |
Copy and balance a cool file. |
|
1 |
cooler_cload_tabix |
Create a cool file from a tabix-indexed contact file and a list of genomic bins. |
|
1 |
cooler_makebins |
Generate fixed-width genomic bins. |
|
1 |
Coordinates of ROI |
|
|
2 |
Copernicus Atmosphere Data Store |
for retrieving data from the Atmosphere Monitoring Service |
Data retrieval
Format detection
Formatting
|
1 |
Copernicus Climate Data Store |
for retrieveing climate data |
Data retrieval
Format detection
Formatting
|
1 |
Copernicus Essential Climate Variables |
for assessing climate variability |
Data retrieval
Format detection
Formatting
|
2 |
Core microbiome |
from a taxonomic OTUreporter |
|
1 |
coronaSPAdes |
SARS-CoV-2 de novo genome assembler |
|
6 |
Corr.axes |
correlation of data to axes |
|
5 |
Correct genotype for STR errors |
that occur during sequencing and library prep |
|
1 |
correctGCBias |
uses the output from computeGCBias to generate GC-corrected BAM/CRAM files |
|
16 |
Corrector AR |
- corrects sequencing errors in short reads |
|
1 |
Corrector HA |
- corrects sequencing errors in short reads |
|
1 |
Corrector1 |
- corrects sequencing errors in short reads |
|
1 |
Correlation |
for numeric columns |
|
1 |
Correlation Plot |
based on a dataframe |
|
1 |
Correlations |
between Taxonomic OTU reporter and Environmental variables. |
|
1 |
Cosine Content |
- measure the cosine content of the PCA projection |
|
4 |
Count |
occurrences of each record |
|
2 |
Count |
- prepare HGDP data for SmileFinder |
|
1 |
Count Aligned Amplicons |
|
|
1 |
Count Covariates |
on BAM files |
|
1 |
Count GFF Features |
|
|
2 |
Count intervals in one file overlapping intervals in another file |
|
|
2 |
Count Objects |
in labled images |
|
1 |
Count reads in features with htseq-count |
- Create a digital expression matrix by counting reads in features with htseq-count |
|
1 |
Count sequences |
Count the sequences in a fasta file |
|
2 |
Count taxnomic numbers |
based on a a taxnomic otu reporter |
|
1 |
Count.groups |
counts the number of sequences represented by a specific group or set of groups |
|
5 |
Count.seqs |
(aka make.table) counts the number of sequences represented by the representative |
|
5 |
count_clustersize |
Get cluster size DNAclust output |
|
1 |
Count_seqs |
in file(fasta/fastq). |
|
1 |
Count_Sig_table |
from a combined statistic table |
|
1 |
CountFrameShift |
based on blastx analysis |
|
1 |
CountRatio |
calculate the log2 of ratio of counts seperated by the taxrank and value. |
|
1 |
CountRelativeAbundance |
Count the number of taxa with a minimum relative abundace. |
|
1 |
Coverage |
of a set of intervals on second set of intervals |
Comparison
Filtering
|
5 |
Coverage Distributions |
: Examine sequence coverage for SNPs |
|
2 |
CoverM-CONTIG |
|
|
1 |
CoverM-GENOME |
read coverage and relative abundance calculator focused on metagenomics applications |
|
1 |
cpgplot |
Plot CpG rich areas |
|
5 |
cpgreport |
Reports all CpG rich regions |
|
5 |
cram-to-bam |
converter |
|
2 |
Create a BedGraph of genome coverage |
|
|
3 |
Create a deep learning model architecture |
using Keras |
|
6 |
Create a genus level gene families file |
|
|
4 |
Create a histogram of genome coverage |
|
|
3 |
Create a model to recommend tools |
using deep learning |
|
5 |
Create a plot from GLM data |
as temporal trend |
|
1 |
Create assemblies with Unicycler |
pipeline for bacterial genomes |
Genome assembly
|
10 |
Create config file |
Create config file |
|
1 |
Create Decoy Database (reverse) |
Creates a decoy search database by adding reverse sequences to an existing database |
|
1 |
Create deep learning model |
with an optimizer, loss function and fit parameters |
|
6 |
Create fasta and tree files (dev version) |
|
|
1 |
Create Frankenstein ligand |
for docking active site definition |
|
3 |
Create GROMACS index files |
using make_ndx |
|
4 |
Create GROMACS position restraints files |
using genrestr |
|
4 |
Create InterMine Interchange |
Dataset |
|
1 |
Create new image |
|
|
2 |
Create or Update Organism |
will create the organism if it doesn't exist, and update otherwise |
|
9 |
Create phyloseq object |
from dada2 sequence and taxonomy tables |
|
1 |
Create single interval |
as a new dataset |
|
1 |
Create text file |
with recurring lines |
|
9 |
Create.database |
creates a database file from a list, repnames, repfasta and contaxonomy file |
|
5 |
CreateMatrix |
Create Genotyping Matrix |
|
1 |
CreateMatrixMultiple |
Create Global Genotyping Matrix |
|
1 |
CRISPR Recognition Tool |
(CRT) |
|
2 |
CRISPR Studio |
facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect |
|
1 |
Cross-contamination Barcode Filter |
for use in plate-based barcoded analyses |
|
3 |
CrossMap BAM |
Convert genome coordinates or annotation files between genome assemblies |
|
5 |
CrossMap BED |
Convert genome coordinates or annotation files between genome assemblies |
|
5 |
CrossMap BigWig |
Convert genome coordinates or annotation files between genome assemblies |
|
1 |
CrossMap GFF |
Convert genome coordinates or annotation files between genome assemblies |
|
5 |
CrossMap region |
Convert genome coordinates or annotation files between genome assemblies |
|
2 |
CrossMap VCF |
Convert genome coordinates or annotation files between genome assemblies |
|
4 |
CrossMap Wig |
Convert genome coordinates or annotation files between genome assemblies |
|
4 |
CryptoGenotyper |
classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data. |
|
1 |
CSV Parser |
Parse the CSV result file generate by mzidLib CSV converter |
|
1 |
CSV to Tabular |
|
|
1 |
csv-to-tabular |
converter |
|
1 |
CTD |
analysis of chemicals, diseases, or genes |
|
1 |
CTSM/FATES-EMERALD |
Functionally Assembled Terrestrial Ecosystem Simulator |
Ecological modelling
Modelling and simulation
|
2 |
Cuffcompare |
compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments |
|
8 |
Cuffdiff |
find significant changes in transcript expression, splicing, and promoter use |
|
11 |
Cufflinks |
transcript assembly and FPKM (RPKM) estimates for RNA-Seq data |
|
8 |
Cuffmerge |
merge together several Cufflinks assemblies |
|
8 |
Cuffnorm |
Create normalized expression levels |
|
7 |
Cuffquant |
Precompute gene expression levels |
|
4 |
cummeRbund |
visualize Cuffdiff output |
|
3 |
Curve Fitting |
to data points using (1st- or 2nd-degree) polynomial function |
|
3 |
cusp |
Create a codon usage table |
|
5 |
Customize the marker sequences and metadata |
from the MetaPhlAn database |
Nucleic acid sequence analysis
Phylogenetic analysis
|
6 |
CustomProDB |
Generate protein FASTAs from exosome or transcriptome data |
|
2 |
Cut |
columns from a table |
Filtering
|
2 |
Cut |
columns from a table (cut) |
|
9 |
Cutadapt |
Remove adapter sequences from FASTQ/FASTA |
Sequence editing
|
22 |
cutClust |
Remove clusters below a certain depth |
|
1 |
cuteSV |
detects long-read-based SVs |
|
1 |
cutseq |
Removes a specified section from a sequence |
|
5 |
CWPair2 |
find matched pairs and unmatched orphans |
|
2 |
D) Plot Cladogram |
|
|
1 |
dada2: assignTaxonomy and addSpecies |
Learn Error rates |
|
6 |
dada2: dada |
Remove sequencing errors |
|
6 |
dada2: filterAndTrim |
Filter and trim short read data |
|
6 |
dada2: learnErrors |
Learn Error rates |
|
6 |
dada2: makeSequenceTable |
construct a sequence table (analogous to OTU table) |
|
6 |
dada2: mergePairs |
Merge denoised forward and reverse reads |
|
6 |
dada2: plotComplexity |
Plot sequence complexity profile |
|
6 |
dada2: plotQualityProfile |
plot a visual summary of the quality scores |
|
6 |
dada2: removeBimeraDenovo |
Remove bimeras from collections of unique sequences |
|
6 |
dada2: sequence counts |
|
|
6 |
DAI Filter: |
Select neoepitopes based on Differential Agretopic Index |
|
1 |
dan |
Calculates DNA RNA/DNA melting temperature |
|
5 |
Data distribution |
analysis using PDFs of normal,lognormal,logistic and gamma. |
|
1 |
Data Fetch |
|
Query and retrieval
|
1 |
Data transformation |
using log, byrow and bycol. |
|
1 |
Datamash |
(operations on tabular data) |
|
5 |
DAVID |
functional annotation for a list of genes |
|
1 |
DBKit Create |
database |
|
1 |
DBKit Create |
database |
|
1 |
DBKit Extract |
entries |
|
1 |
DBKit Extract |
entries |
|
1 |
DBKit Merge |
two databases |
|
1 |
DBKit Merge |
two databases |
|
1 |
dbnsfp.tabular-to-snpsiftdbnsfp |
converter |
|
3 |
dbSNP Filter: |
Select SNVs that are not in dbSNP |
|
1 |
DC Genotyper |
|
|
1 |
DCCM analysis |
- Dynamical Cross-Correlation Maps using Bio3D (DCCM) |
|
2 |
DCS mutations to SSCS stats: |
Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies |
|
3 |
DCS mutations to tags/reads: |
Extracts all tags that carry a mutation in the duplex consensus sequence (DCS) |
|
3 |
dcTMD friction correction |
for calculating friction and free energy profiles from TMD ensembles |
|
2 |
DE |
Performs differential pathway activity analysis using pathway expressions generated from the EMPathways pipeline |
|
1 |
De Nova |
assembler of RNA-seq. |
|
1 |
Decompress an archive |
in zip, gz, tgz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2 format |
|
2 |
DecorateTree |
assign background color to a tree. |
|
1 |
Deep learning training and evaluation |
conduct deep training and evaluation either implicitly or explicitly |
|
4 |
DeepVariant |
deep learning-based variant caller |
Variant calling
|
3 |
Degap.seqs |
Remove gap characters from sequences |
|
5 |
degapseq |
Removes gap characters from sequences |
|
5 |
Delete all annotations from an Apollo record |
|
|
8 |
Delete an Apollo record |
|
|
8 |
Delete Overlapping Indels |
from a chromosome indels file |
|
1 |
Delete/select Columns |
From a data frame. |
|
1 |
Deletion Profile |
calculates the distributions of deleted nucleotides across reads |
|
6 |
Delines |
Delete line(s) from a file |
|
1 |
Delly call |
and genotype structural variants |
|
5 |
Delly classify |
somatic or germline copy-number variants |
|
3 |
Delly cnv |
discover and genotype copy-number variants |
|
3 |
Delly filter |
somatic or germline structural variants |
|
5 |
Delly long-read (lr) |
optimized calling and genotyping of structural variants |
|
6 |
Delly merge |
structural variants across/within BCF/VCF file(s) |
|
5 |
Delta-Filter |
Filters alignment (delta) file from nucmer |
Read mapping
Sequence alignment
|
5 |
Demultiplex |
Demultiplex reads for submission: FASTQ format |
|
1 |
Demultiplex (dev version) |
Demultiplex reads for submission: FASTQ format |
|
1 |
Denoise_16S_rRNA |
of a fasta query file |
|
1 |
DenoiseAmplicon |
remove amplicon or chimera artifacts |
|
1 |
Depth of Coverage |
on BAM files |
|
3 |
Depth of Coverage |
on BAM files |
|
1 |
Dereplicate |
Remove duplicate sequences |
|
1 |
Describe samples |
and replicates |
|
11 |
Descriptors |
calculated with RDKit |
|
1 |
Descriptors |
calculated with RDKit |
|
4 |
descseq |
Alter the name or description of a sequence |
|
5 |
DESeq |
Determines differentially expressed transcripts from read alignments |
|
1 |
DESeq2 |
Determines differentially expressed features from count tables |
Differential gene expression profiling
RNA-Seq quantification
|
22 |
DESeq2 |
Differential gene expression analysis based on the negative binomial distribution |
|
1 |
detect CRISPR sequences |
(minced) |
|
1 |
Detection Visualization |
Detection Visualization |
|
3 |
Determine distance to defined points |
- determine the minimum distances between a molecule and a set of 3D points |
|
2 |
Determine_batch_correction |
to choose between linear, lowess and loess methods |
|
4 |
Deunique.seqs |
Return all sequences |
|
5 |
Deunique.tree |
Reinsert the redundant sequence identiers back into a unique tree. |
|
5 |
DEXSeq |
Inference of differential exon usage in RNA-Seq |
|
1 |
DEXSeq |
Determines differential exon usage from count tables |
|
10 |
DEXSeq-Count |
Prepare and count exon abundancies from RNA-seq data |
|
10 |
DFPostHSDPvals |
calculated pairwise p-values using different posthoc tests. |
|
1 |
DIA_Umpire_SE |
DIA signal extraction |
|
1 |
DIAlignR |
for retention time alignment of targeted mass spectrometric data |
|
1 |
Diamond |
alignment tool for short sequences against a protein database |
Sequence alignment analysis
|
9 |
Diamond |
a blastx/n programe to analyze large datsets. |
|
1 |
Diamond makedb |
Build database from a FASTA file |
Sequence alignment analysis
|
8 |
Diamond view |
generate formatted output from DAA files |
Sequence alignment analysis
|
6 |
diapysef library generation |
generates spectral library for DIA analysis |
|
1 |
diff |
analyzes two files and generates an unidiff text file with information about the differences and an optional Html report |
|
3 |
Diffacto |
Comparative Protein Abundance from Covariation of Peptide Abundances |
|
1 |
DiffBind |
differential binding analysis of ChIP-Seq peak data |
|
12 |
DifferenntKEGGmapsbetweenTreatments |
map the pathways based on mapped. |
|
1 |
Differential Cleavage |
: Select SNPs differentially cut by specified restriction enzymes |
|
2 |
Differential expression analysis |
using a Trinity assembly |
|
1 |
Differential expression analysis |
using a Trinity assembly |
|
11 |
Differential_Count |
models using BioConductor packages |
|
2 |
diffseq |
Find differences between nearly identical sequences |
|
5 |
digest |
Protein proteolytic enzyme or reagent cleavage digest |
|
5 |
Digest |
Theoretically digest all protein sequences from a FASTA file by trypsin |
|
1 |
Dihedral Analysis |
Time series of dihedrals |
|
5 |
DISCO |
to assemble metagenomics data using an overlap-layout-consensus (OLC) approach |
|
2 |
DiscoSnp++ |
is an efficient tool for detecting SNPs without a reference genome. |
|
5 |
DiscoSnpRAD |
discovering polymorphism from raw unassembled RADSeq NGS reads. |
|
4 |
Discriminant Analysis |
|
|
12 |
Display |
database release and linked database informations KEGG(www.kegg.jp) |
|
1 |
DisplayDataOnImage |
produce an image with data on top of identified objects |
|
2 |
Dist.seqs |
calculate uncorrected pairwise distances between aligned sequences |
|
5 |
Dist.shared |
Generate a phylip-formatted dissimilarity distance matrix among multiple groups |
|
5 |
Distance Analysis |
- time series using MDAnalysis |
|
5 |
Diversity |
: pi, allowing for unsequenced intervals |
|
2 |
Divide FASTQ file into paired and unpaired reads |
using the read name suffixes |
|
1 |
DMGeneIdConverter |
D. melanogaster gene ID conversion |
|
1 |
dnaclust |
Cluster sequences into OTUs using DNAclust |
|
1 |
dnaclust2tab |
Convert dnaclust to tabular |
|
1 |
DNAdiff |
Evaluate similarities/differences between two sequences |
Read mapping
Sequence alignment
|
5 |
Dominat Taxa |
which is present in the current taxonomic OTU report |
|
1 |
DotKnot |
pseudoknot prediction in a given RNA sequence |
|
1 |
dotmatcher |
Displays a thresholded dotplot of two sequences |
|
5 |
dotpath |
Non-overlapping wordmatch dotplot of two sequences |
|
5 |
dottup |
Displays a wordmatch dotplot of two sequences |
|
5 |
Download |
Sequences from uniport based on uniport id. |
|
1 |
Download and Extract Reads in BAM |
format from NCBI SRA |
Data retrieval
Formatting
|
24 |
Download and Extract Reads in FASTQ |
format from NCBI SRA |
Data retrieval
Formatting
|
20 |
Download and Generate Pileup Format |
from NCBI SRA |
|
9 |
Download run data |
from EBI Metagenomics database |
|
1 |
Download_Seq_From_NCBI |
based on an file with all accession numbers. |
|
1 |
DownLoadSeqFromNCBI |
using id files |
|
1 |
Downsample SAM/BAM |
Downsample a file to retain a subset of the reads |
|
14 |
dpocket |
to calculate descriptors for protein pockets |
|
1 |
Dr. Disco (bam-extract) |
Extracts reads from two targeted regions |
|
1 |
Dr. Disco (classify) |
Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists |
|
1 |
Dr. Disco (detect) |
Detects break-points in RNA-seq |
|
1 |
Dr. Disco (fix) |
Fixes chimeric alignments from STAR |
|
1 |
Dr. Disco (integrate) |
Merges corresponding genomic breaks and exon-to-exon junctions |
|
1 |
Draw nucleotides distribution chart |
|
|
4 |
Draw phylogeny |
|
|
1 |
Draw quality score boxplot |
for SOLiD data |
|
1 |
Draw quality score boxplot |
|
|
4 |
Draw ROC plot |
on "Perform LDA" output |
|
2 |
Draw Stacked Bar Plots |
for different categories and different criteria |
|
1 |
Draw variants |
: show positions of SNVs and unsequenced intervals |
|
2 |
dreg |
Regular expression search of a nucleotide sequence |
|
6 |
dRep compare |
compare a list of genomes |
|
3 |
dRep dereplicate |
De-replicate a list of genomes |
|
3 |
Droplet barcode rank plot |
Creates a barcode rank plot for quality control of droplet single-cell RNA-seq data |
|
3 |
DropletUtils |
Utilities for handling droplet-based single-cell RNA-seq data |
DNA barcoding
Parsing
|
9 |
DropletUtils emptyDrops |
Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment. |
|
2 |
DropletUtils Read10x |
into SingleCellExperiment object |
|
3 |
Drug-likeness |
quantitative estimation (QED) with RDKit |
|
4 |
DrugBankAnnotator |
Retrieve information from DrugBank |
|
1 |
Du Novo: Align families |
of duplex sequencing reads |
|
10 |
Du Novo: Check input |
for family content |
|
3 |
Du Novo: Correct barcodes |
of duplex sequencing reads |
|
11 |
Du Novo: Make consensus reads |
from duplex sequencing alignments |
|
10 |
Du Novo: Make families |
of duplex sequencing reads |
|
10 |
E) Plot One Feature |
|
|
1 |
EBI SCXA Data Retrieval |
Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA) |
|
2 |
EBI Search |
to obtain search results on resources and services hosted at the EBI |
|
2 |
ectyper |
ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. |
|
1 |
Edena (assembling) |
|
|
1 |
Edena (overlapping) |
|
|
1 |
edgeR |
- Estimates differential gene expression for short read sequence count using methods appropriate for count data |
|
2 |
edgeR |
Perform differential expression of count data |
Differential gene expression profiling
RNA-seq read count analysis
|
10 |
EGA Download Client |
|
|
5 |
EGA Download streamer |
data from the European Genome-phenome Archive in a secure manner |
|
1 |
eggNOG Mapper |
functional sequence annotation by orthology |
|
10 |
EGSEA |
easy and efficient ensemble gene set testing |
|
4 |
einverted |
Finds DNA inverted repeats |
|
5 |
emPAI analysis in X-Tracker |
Execute emPAI quantitation method within X-Tracker |
|
1 |
EMPathways |
Quantifies metabolic pathway activity levels from metatranscriptomic data by Expectation-Maximization |
|
1 |
ENA Upload tool |
|
|
9 |
EncyclopeDIA |
Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data |
|
3 |
EncyclopeDIA Quantify |
samples from Data-Independent Acquisition (DIA) MS/MS Data |
|
3 |
End-to-End Analysis |
- End-to-End distance timeseries and histogram for the given selections |
|
2 |
EndvMapHugo |
Maps Endv ENSMBL to HUGO |
|
1 |
Enhance contrast |
|
|
2 |
EnhanceOrSuppressFeatures |
to improve subsequent identification of objects |
|
2 |
Enrichment |
analysis of pathway,genesets or taxonomic group |
|
1 |
ensembl_to_ucsc |
convert interval format |
|
1 |
Ensemble methods |
for classification and regression |
|
12 |
Enumerate changes |
calculated with Dimorphite DL and RDKit |
|
2 |
EODIE |
converts simple features data between file formats |
|
1 |
ep2P |
ep2P |
|
1 |
ePCR |
analysis of batch sequence data |
|
1 |
epestfind |
Finds PEST motifs as potential proteolytic cleavage sites |
|
5 |
EpiCSeg - Chromatin segmentation |
|
|
1 |
equicktandem |
Finds tandem repeats |
|
5 |
Escape Excel |
- Protect files from auto-conversion in Excel |
|
1 |
EsGecopyPerBillion |
estimate gene copy numbers in per billion reads. |
|
1 |
est2genome |
Align EST and genomic DNA sequences |
|
5 |
Estimate Abundance at Taxonomic Level |
Bayesian Reestimation of Abundance with KrakEN |
Statistical calculation
|
3 |
Estimate Indel Rates |
for 3-way alignments |
|
1 |
Estimate Library Complexity |
|
|
3 |
Estimate microsatellite mutability |
by specified attributes |
|
1 |
Estimate substitution rates |
for non-coding regions |
|
1 |
Estimate temporal population evolution |
by species |
|
2 |
Estimate temporal population variation |
by specialization group |
|
3 |
estimate-energy |
Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place |
|
2 |
EstimateLibraryComplexity |
assess sequence library complexity from read sequences |
|
14 |
estimateReadFiltering |
estimates the number of reads that would be filtered given certain criteria |
|
6 |
Estimator attributes |
get important attributes from an estimator or scikit object |
|
9 |
etandem |
Looks for tandem repeats in a nucleotide sequence |
|
5 |
ETE GeneTree splitter |
from a genetree using the ETE Toolkit |
|
7 |
ETE lineage generator |
from a list of species/taxids using the ETE Toolkit |
|
5 |
ETE mod |
manipulates tree topology by rooting, pruning or sorting branches |
|
4 |
ETE species tree generator |
from a list of species using the ETE Toolkit |
|
4 |
ETE taxa DB generator |
generates the ETE sqlite DB from the NCBI taxdump.tar.gz |
|
4 |
Eval Variants |
|
|
3 |
Eval Variants |
|
|
1 |
Evaluate a Fitted Model |
using a new batch of labeled data |
|
6 |
Evaluate pairwise distances |
or compute affinity or kernel for sets of samples |
|
12 |
Evaluate the probability of the allele combination to generate read profile |
|
|
1 |
ExcelSearch |
Search excel files for geneIDs |
|
1 |
ExecEndeavour |
Runs Endeavour |
|
1 |
Execute an SPARQL query against an OWL ontology |
It executes an SPARQL query against the input OWL ontology and generates a two column tab file with the variables and bound entities |
|
1 |
ExomeDepth |
Calls copy number variants (CNVs) from targeted sequence data |
|
1 |
Exonerate |
pairwise sequence comparison |
|
4 |
Exonerate2Apollo |
Transform a Exonerate GFF to a WebApollo compliant GFF |
|
1 |
Expected temporal trend |
of species abundance |
|
1 |
Expected temporal trend |
of species abundance |
|
1 |
Export AnnData and loom files |
Interconvert AnnData and Loom formats |
|
10 |
Export datasets |
to remote files source |
|
1 |
Export to GraPhlAn |
|
|
2 |
ExportToSpreadsheet |
export measurements into one or more files |
|
2 |
eXpress |
Quantify the abundances of a set of target sequences from sampled subsequences |
|
2 |
Extract |
reads from a specified region |
|
1 |
Extract ACGT |
from scaffolds |
|
1 |
Extract and cluster differentially expressed transcripts |
from a Trinity assembly |
|
12 |
Extract clusters of MD trajectories |
from linkage matrix data |
|
3 |
Extract CuffDiff |
tabular files from a cummeRbund database |
|
2 |
Extract DNA sequence from GTF files |
Write a fasta file with spliced exons for each GFF transcript |
|
1 |
Extract element identifiers |
of a list collection |
|
2 |
Extract energy components with GROMACS |
|
|
7 |
Extract FASTA from coding sequences in barley |
using BLAST |
|
1 |
Extract FASTA from coding sequences in rye |
using BLAST |
|
1 |
Extract FASTA from coding sequences in wheat |
using BLAST |
|
1 |
Extract FASTA from coding sequences in wheat pan genomes |
using BLAST |
|
1 |
Extract FASTA from pseudomolecules in barley |
using BLAST |
|
1 |
Extract FASTA from pseudomolecules in barley |
using BLAST |
|
1 |
Extract FASTA from pseudomolecules in rye |
using BLAST |
|
1 |
Extract FASTA from pseudomolecules in wheat |
using BLAST |
|
1 |
Extract FASTA from pseudomolecules in wheat pan genome |
using BLAST |
|
1 |
Extract FASTQ |
in tabular format from a set of FAST5 files |
|
2 |
Extract features |
from GFF data |
|
1 |
Extract Genomic DNA |
using coordinates from assembled/unassembled genomes |
|
7 |
Extract MAF blocks |
given a set of genomic intervals |
|
4 |
Extract MAF by block number |
given a set of block numbers and a MAF file |
|
1 |
Extract nanopore events |
from a set of sequencing reads |
|
2 |
Extract nucleotide range and flanking sequences |
Get FASTA sequences from BED interval |
|
1 |
Extract orthologous microsatellites |
for multiple (>2) species alignments |
|
1 |
Extract Orthologous Microsatellites |
from pair-wise alignments |
|
1 |
Extract Pairwise MAF blocks |
given a set of genomic intervals |
|
1 |
Extract reads |
in FASTA or FASTQ format from nanopore files |
|
2 |
Extract RMSD distance matrix data |
from MD ensemble with MDAnalysis |
|
3 |
Extract the marker sequences and metadata |
from the MetaPhlAn database |
Nucleic acid sequence analysis
Phylogenetic analysis
|
6 |
Extract time |
and channel information from a set of FAST5 files |
|
2 |
Extract top view |
from whole-slice image |
|
2 |
Extract values from an SD-file |
into a tabular file using RDKit |
|
4 |
extract-boxed-sequences |
Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility |
|
2 |
extractfeat |
Extract features from a sequence |
|
5 |
Extracting Topology Information |
from a GROMACS topology file |
|
1 |
extractseq |
Extract regions from a sequence |
|
5 |
extractseq |
Extract Sequence around variant position |
|
1 |
F) Plot Differential Features |
|
|
1 |
fargene |
Fragmented antibiotic resistance gene identifier |
|
2 |
faSplit |
Split a FASTA file |
|
3 |
Fasta Extract Sequence |
Extract a single sequence from a fasta file. |
|
2 |
FASTA from allele counts |
Generate major and minor allele sequences from alleles table |
|
1 |
Fasta Header Manipulation |
Extracts part of the original header or converts to a shorter header |
|
1 |
FASTA Merge Files and Filter Unique Sequences |
Concatenate FASTA database files together |
|
4 |
Fasta nucleotide color plot |
|
|
2 |
Fasta Statistics |
Display summary statistics for a fasta file. |
|
5 |
Fasta to Bed File |
Create Bed file from Multiple fasta file |
|
1 |
FASTA Width |
formatter |
|
3 |
fasta-to-fai |
converter |
|
1 |
FASTA-to-Tabular |
converter |
|
3 |
Fasta2Fasta |
retrieve fasta seqs from the reference using the ids from the other fasta. |
|
1 |
fasta_to_gspan |
|
|
3 |
FastaCLI |
Appends decoy sequences to FASTA files |
|
6 |
fastaGroomerForMakeBlastdb |
fasta Groomer For MakeBlastdb |
|
2 |
FastANI |
fast alignment-free computation of whole-genome Average Nucleotide Identity |
|
1 |
FastaQContig |
make contigs using forward and reverse fastaq sequences |
|
1 |
fastaselectclust |
Get Fasta file of cluster centres from DNAclust output |
|
1 |
Faster Download and Extract Reads in FASTQ |
format from NCBI SRA |
Data retrieval
Formatting
|
15 |
FASTG2Protlib-Peptides |
Generate FASTA from FASTG |
|
1 |
FASTG2Protlib-Validate |
Validate a candidate protein library |
|
1 |
Fastidx |
fasta to .fastIdx index |
|
1 |
fastp |
- fast all-in-one preprocessing for FASTQ files |
|
8 |
fastpca |
- dimensionality reduction of MD simulations |
|
2 |
FASTQ de-interlacer |
on paired end reads |
Splitting
|
5 |
FASTQ Groomer |
convert between various FASTQ quality formats |
Sequence conversion
|
5 |
FASTQ info |
validates single or paired fastq files |
Format validation
|
1 |
FASTQ interlacer |
on paired end reads |
Aggregation
|
6 |
FASTQ joiner |
on paired end reads |
Aggregation
|
7 |
FASTQ Masker |
by quality score |
Sequence masking
|
5 |
FASTQ Quality Trimmer |
by sliding window |
|
5 |
FASTQ QualityConverter |
convert from various base-FASTQ quality formats to fastqsanger |
|
1 |
FastQ Screen |
for contamination |
|
2 |
FASTQ splitter |
on joined paired end reads |
Splitting
|
6 |
FASTQ Summary Statistics |
by column |
Sequence assembly validation
|
4 |
FASTQ to FASTA |
converter from FASTX-toolkit |
Sequence conversion
|
6 |
FASTQ to FASTA |
converter |
Conversion
|
5 |
FASTQ to Tabular |
converter |
Sequence conversion
|
5 |
FASTQ Trimmer |
by column |
Sequence trimming
|
5 |
fastq-join |
- Joins two paired-end reads on the overlapping ends |
|
3 |
Fastq.info |
Convert fastq to fasta and quality |
|
6 |
fastq2fasta |
Convert fastq to fasta |
Sequence conversion
|
2 |
FastQC |
Read Quality reports |
Sequence composition calculation
Sequencing quality control
Statistical calculation
|
18 |
FastqChecker |
check the rawdata of fastq files. |
|
1 |
FastqCounter |
counts read number in fastq libraries. |
|
1 |
FASTQE |
visualize fastq files with emoji's 🧬😎 |
|
5 |
FastqFilter |
Filter low quality sequences in a fastq library. |
|
1 |
fastqillumina-to-fqtoc |
converter |
|
1 |
FastqMcf |
sequence quality filtering and clipping |
|
1 |
FASTQSOLEXA-to-FASTA-QUAL |
extracts sequences and quality scores from FASTQSOLEXA data |
|
1 |
FastqToSam |
convert Fastq data into unaligned BAM |
|
19 |
FASTTREE |
build maximum-likelihood phylogenetic trees |
Phylogenetic analysis
Phylogenetic inference (from molecular sequences)
|
4 |
FastTree |
construct phylogenetic tree based on aligned DNA or AA sequences. |
|
1 |
FDR filter |
|
|
1 |
Feature coverage |
|
|
1 |
Feature Selection |
module, including univariate filter selection methods and recursive feature elimination algorithm |
|
12 |
featureCounts |
Measure gene expression in RNA-Seq experiments from SAM or BAM files. |
Sequence assembly
|
25 |
FEELnc |
FlExible Extraction of LncRNA |
|
6 |
Fetch bases flanking |
the STRs in the reads and output two fastq files in forward-forward orientation |
|
1 |
Fetch closest non-overlapping feature |
for every interval |
Filtering
|
4 |
Fetch Indels |
from 3-way alignments |
|
1 |
Fetch Indels |
from pairwise alignments |
|
1 |
Fetch NCBI Entrez |
Fetch NCBI database with an Entrez query |
|
1 |
Fetch substitutions |
from pairwise alignments |
|
2 |
Fetch taxonomic representation |
|
|
2 |
fgsea |
- fast preranked gene set enrichment analysis |
|
3 |
Files_2_FTP |
Copy Files to your FTP account for easy download |
|
1 |
Filter |
data on any column using simple expressions |
Formatting
|
2 |
Filter |
a VCF file |
|
1 |
Filter |
a set of molecules from a file |
|
1 |
Filter |
a set of molecules from a file |
|
6 |
Filter |
with scanpy |
|
7 |
Filter - Blur |
Apply a blur filter on the image. |
|
1 |
Filter - Contour |
Apply a contour filter on image. |
|
1 |
Filter - Detail |
Apply a detail filter on image. |
|
1 |
Filter - Edge Enhance |
Apply an edge_enhance filter on the image. |
|
1 |
Filter - Edge Enhance More |
Apply an edge_enhance_more filter on the image. |
|
1 |
Filter - Emboss |
Apply an emboss filter on image. |
|
1 |
Filter - Find Edges |
Apply find_edges filter on the image. |
|
1 |
Filter - Invert |
Apply an invert filter on the image. |
|
1 |
Filter - Max |
Apply a max filter of the given size. |
|
1 |
Filter - Median |
Apply a median filter of the given size. |
|
1 |
Filter - Min |
Apply a min filter of the given size. |
|
1 |
Filter - Mode |
Apply a mode filter of the given size. |
|
1 |
Filter - Sharpen |
Apply a sharpen filter on image. |
|
1 |
Filter - Smooth |
Apply a smooth filter on the image. |
|
1 |
Filter - Smooth More |
Apply a smooth_more filter on the image. |
|
1 |
Filter and merge |
chimeric reads from Arima Genomics |
|
1 |
Filter BAM |
datasets on a variety of attributes |
|
6 |
Filter BED on splice junctions |
that are not in a reference bed file |
|
1 |
Filter by quality |
|
Filtering
|
6 |
Filter CDS and protein FASTA Faba bean |
on the headers and/or the sequences |
|
1 |
Filter Combined Transcripts |
using tracking file |
|
1 |
Filter FASTA |
|
|
1 |
Filter FASTA |
on the headers and/or the sequences |
|
5 |
Filter FASTQ |
reads by quality score and length |
Filtering
|
4 |
Filter GFF data by attribute |
using simple expressions |
|
2 |
Filter GFF data by feature count |
using simple expressions |
|
1 |
Filter GTF data by attribute values_list |
|
|
2 |
Filter Image |
applies a standard filter to an image |
|
2 |
Filter low expression transcripts |
from a Trinity assembly |
|
11 |
Filter MAF |
by specified attributes |
|
1 |
Filter MAF blocks |
by Size |
|
1 |
Filter MAF blocks |
by Species |
|
1 |
Filter mapped reads |
on MD tag string |
|
1 |
Filter nucleotides |
based on quality scores |
|
1 |
Filter pileup |
on coverage and SNPs |
|
3 |
Filter SAM |
on bitwise flag values |
|
1 |
Filter SAM or BAM |
files on FLAG MAPQ RG LN or by region |
Filtering
Nucleic acid sequence analysis
|
2 |
Filter SAM or BAM, output SAM or BAM |
files on FLAG MAPQ RG LN or by region |
|
6 |
Filter segmentation |
Filter segmentation by rules |
|
1 |
Filter sequences by ID |
from a tabular file |
|
5 |
Filter sequences by length |
|
Filtering
|
6 |
Filter sequences by mapping |
from SAM/BAM file |
|
4 |
Filter SNPs |
: Discard some SNPs based on coverage, quality or spacing |
|
4 |
Filter SPAdes output |
remove low coverage and short contigs/scaffolds |
|
1 |
Filter species |
with rare and low abundances |
|
2 |
Filter Tabular |
|
|
5 |
Filter with SortMeRNA |
of ribosomal RNAs in metatranscriptomic data |
|
6 |
filter-annotated-entries |
Split entries into two files based on whether they overlap annotations in a bed file |
|
2 |
filter-by-energy |
Split entries over two files based on the estimated energy |
|
2 |
Filter.seqs |
removes columns from alignments |
|
5 |
Filter.shared |
remove OTUs based on various critieria |
|
6 |
filterRatio |
Filter Ratio |
|
1 |
filtersam_mapped_and_unique |
Filter SAM file for uniq and well mapped pair-end reads |
|
1 |
FilterSamReads |
include or exclude aligned and unaligned reads and read lists |
|
14 |
filtlong |
Filtering long reads by quality |
|
3 |
FIMO |
- Scan a set of sequences for motifs |
|
12 |
Find |
relatied entries by using database cross-reference in KEGG(www.kegg.jp) |
|
1 |
Find |
adverse drug-drug interactions from KEGG(www.kegg.jp) |
|
1 |
Find |
entries with matching query keyword or other query data from KEGG(www.kegg.jp) |
|
1 |
Find diagnostic hits |
|
|
1 |
Find edges |
|
|
2 |
find in reference |
filter peptides that are present in proteins |
|
4 |
Find lowest diagnostic rank |
|
|
1 |
Find maxima |
|
|
2 |
Find Nested Alternate ORFs (nAlt-ORFs) |
from BED and 2bit/FASTA |
Coding region prediction
Codon usage analysis
Codon usage table generation
Genome annotation
|
1 |
find-boxes |
Finds all occurances of two given boxes (sequence motifs) within a FASTA file |
|
2 |
findMotifsGenome |
|
|
3 |
Finds SNP sites |
from a multi-FASTA alignment file |
|
1 |
Fit a BUM model |
with p-values |
|
2 |
Fit a Pipeline, Ensemble |
or other models using a labeled dataset |
|
6 |
Fit HMM |
on numeric data |
|
1 |
fix-fasta-headers |
Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file |
|
2 |
FixMateInformation |
ensure that all mate-pair information is in sync between each read and it's mate pair |
|
14 |
FlaiMapper |
detects small ncRNA derived fragments in small RNA-Seq data |
|
1 |
FLAIR collapse |
defines high-confidence isoforms from flair-corrected reads |
|
3 |
FLAIR correct |
corrects misaligned splice sites using genome annotations |
|
2 |
Flanking Sequence |
: Fetch DNA sequence for intervals surrounding the given SNPs |
|
2 |
FLASH |
adjust length of short reads |
|
7 |
Flight curve |
compute the regional expected pattern of abundance |
|
1 |
Flight curve |
compute the regional expected pattern of abundance |
|
1 |
Flye |
de novo assembler for single molecule sequencing reads |
Genome assembly
|
8 |
Fold Change Filter |
Filters IsoDE2 output based on fold change |
|
1 |
footprint |
|
|
1 |
Format Article |
Format an article for DB construction |
|
1 |
Format cd-hit outputs |
to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file |
|
2 |
Format MetaPhlAn2 |
output for Krona |
|
2 |
Format MetaPhlAn2 |
output to extract abundance at different taxonomic levels |
|
2 |
FormatPathogenReporter |
split the subspecies column into species . |
|
1 |
Founders sequenced |
: Offspring estimated heterozygosity from a pedigree with sequenced founders |
|
2 |
FPKM Count |
calculates raw read count, FPM, and FPKM for each gene |
|
8 |
fpocket |
- find potential binding sites in protein structures |
|
4 |
FragGeneScan |
for finding (fragmented) genes in short reads |
|
2 |
freak |
Residue/base frequency table or plot |
|
5 |
FreeBayes |
bayesian genetic variant detector |
|
12 |
Freyja: Aggregate and visualize |
demixed results |
|
1 |
Freyja: Demix |
lineage abundances |
|
1 |
FROGS Abundance normalisation |
Normalize OTUs abundance. |
Standardisation and normalisation
|
5 |
FROGS Affiliation Filters |
Filters OTUs on several affiliation criteria |
|
3 |
FROGS Affiliation OTU |
Taxonomic affiliation of each OTU's seed by RDPtools and BLAST |
Taxonomic classification
|
5 |
FROGS Affiliation postprocess |
Optionnal step to resolve inclusive amplicon ambiguities and to aggregate OTUs based on alignment metrics |
Taxonomic classification
|
5 |
FROGS Affiliations stat |
Process some metrics on taxonomies. |
Taxonomic classification
|
5 |
FROGS BIOM to std BIOM |
Converts a FROGS BIOM in fully compatible BIOM. |
Formatting
|
5 |
FROGS BIOM to TSV |
Converts a BIOM file in TSV file. |
Formatting
|
5 |
FROGS Clustering swarm |
Single-linkage clustering on sequences |
Taxonomic classification
|
5 |
FROGS Clusters stat |
Process some metrics on clusters. |
Clustering
|
5 |
FROGS Demultiplex reads |
Attribute reads to samples in function of inner barcode. |
Classification
|
5 |
FROGS Filters |
Filters OTUs on several criteria. |
Taxonomic classification
|
2 |
FROGS ITSx |
Extract the highly variable ITS1 and ITS2 subregions from ITS sequences. |
Sequence trimming
|
5 |
FROGS OTU Filters |
Filters OTUs on several criteria. |
|
3 |
FROGS Pre-process |
merging, denoising and dereplication. |
Filtering
|
5 |
FROGS Remove chimera |
Remove PCR chimera in each sample. |
Editing
|
5 |
FROGS Tree |
Reconstruction of phylogenetic tree |
Taxonomic classification
|
5 |
FROGS TSV_to_BIOM |
Converts a TSV file in a BIOM file. |
Formatting
|
5 |
FROGSFUNC_step1_placeseqs |
Places the OTUs into a reference phylogenetic tree. |
|
2 |
FROGSFUNC_step2_copynumbers |
Predicts number of marker and function copy number in each OTU. |
|
2 |
FROGSFUNC_step3_functions |
Calculates functions abundances in each sample. |
|
2 |
FROGSFUNC_step4_pathways |
Calculates pathway abundances in each sample. |
|
2 |
FROGSSTAT DESeq2 Preprocess |
import a Phyloseq object and prepare it for DESeq2 differential abundance analysis |
|
3 |
FROGSSTAT Phyloseq Alpha Diversity |
with richness plot |
Taxonomic classification
|
5 |
FROGSSTAT Phyloseq Beta Diversity |
distance matrix |
Taxonomic classification
|
5 |
FROGSSTAT Phyloseq Composition Visualisation |
with bar plot and composition plot |
Taxonomic classification
|
5 |
FROGSSTAT Phyloseq Import Data |
from 3 files: biomfile, samplefile, treefile |
Taxonomic classification
|
5 |
FROGSSTAT Phyloseq Multivariate Analysis Of Variance |
perform Multivariate Analysis of Variance (MANOVA) |
Taxonomic classification
|
5 |
FROGSSTAT Phyloseq Sample Clustering |
of samples using different linkage methods |
Taxonomic classification
|
5 |
FROGSSTAT Phyloseq Structure Visualisation |
with heatmap plot and ordination plot |
Taxonomic classification
|
5 |
FROGSTAT Deseq2 Visualisation |
to extract and visualise differentially abundant OTUs |
|
3 |
FSD Before/After: |
Family Size Distribution of duplex sequencing tags during Du Novo analysis |
|
2 |
FSD regions: |
Family size distribution of user-specified regions in the reference genome |
|
2 |
FSD: |
Family Size Distribution of duplex sequencing tags |
|
2 |
FTPSend |
export history files to your galaxy FTP directory |
|
1 |
FuMa |
match detected fusion genes based on gene names (in particular for RNA-Seq) |
|
1 |
Funannotate assembly clean |
|
|
5 |
Funannotate compare |
annotations |
|
5 |
Funannotate functional |
annotation |
|
5 |
Funannotate predict annotation |
|
|
6 |
Functional Gene |
analysis pipeline for HTS of functional genes. |
|
1 |
FunDO |
human genes associated with disease terms |
|
2 |
fuzznuc |
Nucleic acid pattern search |
|
6 |
fuzzpro |
Protein pattern search |
|
5 |
fuzztran |
Protein pattern search after translation |
|
5 |
g:Profiler |
tools for functional profiling of gene lists |
|
1 |
g:Profiler |
functional enrichment analysis |
|
1 |
GAGE analysis |
- calculate statistics for contigs and scaffolds |
|
1 |
GapCloser 1.10 |
- close gaps in scaffolds |
|
1 |
GapCloser 1.12 |
- close gaps in scaffolds |
|
1 |
Garli |
phylogenetic inference using the maximum-likelihood |
|
1 |
garnier |
Predicts protein secondary structure |
|
5 |
GATK4 Mutect2 |
- Call somatic SNVs and indels via local assembly of haplotypes |
|
8 |
GBK-to-GFF |
converter |
|
1 |
GC Skew |
calculates skew over genomic sequences |
Nucleic acid property calculation
|
10 |
gcoords2cons |
Genomic Coordinates to Consequence types |
|
1 |
Gcoords2gcoords |
Generation and split of genomic coordinates |
|
1 |
gcoords2genes |
Genomic Coordinates to neighbouring Genes |
|
1 |
gcoords2ld |
Pairwise coordinate/gene LD checker |
|
1 |
gcoords2reg |
Retrieval of Ensembl regulatory information |
|
1 |
gcoords2snp |
Genomic Coordinates to SNP |
|
1 |
gcoordsconservation |
Sequence conservation status/GERP scores retriever |
|
1 |
gd_snp to VCF |
: Convert from gd_snp or gd_genotype to VCF format, for submission to dbSNP |
|
2 |
GDAL addo |
builds or rebuilds overview images |
|
2 |
GDAL Build VRT |
builds a VRT from a list of datasets |
|
2 |
GDAL Informations |
lists information about a raster dataset |
|
2 |
GDAL Merge |
mosaics a set of images |
|
2 |
GDAL Translate |
converts raster data between different formats. |
|
2 |
GDAL Warp |
image reprojection and warping utility |
|
2 |
GECCO |
is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs). |
Nucleic acid feature detection
|
3 |
Gecko |
Ungapped genome comparison |
|
3 |
geecee |
Calculates fractional GC content of nucleic acid sequences |
|
5 |
GEMINI actionable_mutations |
Retrieve genes with actionable somatic mutations via COSMIC and DGIdb |
|
4 |
GEMINI amend |
Amend an already loaded GEMINI database. |
|
5 |
GEMINI annotate |
the variants in an existing GEMINI database with additional information |
|
7 |
GEMINI autosomal recessive/dominant |
Find variants meeting an autosomal recessive/dominant model |
|
2 |
GEMINI burden |
perform sample-wise gene-level burden calculations |
|
4 |
GEMINI comp_hets |
Identifying potential compound heterozygotes |
|
2 |
GEMINI database info |
Retrieve information about tables, columns and annotation data stored in a GEMINI database |
|
4 |
GEMINI de_novo |
Identifying potential de novo mutations |
|
2 |
GEMINI dump |
Extract data from the Gemini DB |
|
2 |
GEMINI fusions |
Identify somatic fusion genes from a GEMINI database |
|
5 |
GEMINI gene_wise |
Custom genotype filtering by gene |
|
5 |
GEMINI inheritance pattern |
based identification of candidate genes |
|
2 |
GEMINI interactions |
Find genes among variants that are interacting partners |
|
4 |
GEMINI load |
Loading a VCF file into GEMINI |
|
7 |
GEMINI lof_sieve |
Filter LoF variants by transcript position and type |
|
4 |
GEMINI mendel_errors |
Identify candidate violations of Mendelian inheritance |
|
2 |
GEMINI pathways |
Map genes and variants to KEGG pathways |
|
5 |
GEMINI qc |
Quality control tool |
|
5 |
GEMINI query |
Querying the GEMINI database |
|
5 |
GEMINI region |
Extracting variants from specific regions or genes |
|
2 |
GEMINI roh |
Identifying runs of homozygosity |
|
5 |
GEMINI set_somatic |
Tag somatic mutations in a GEMINI database |
|
5 |
GEMINI stats |
Compute useful variant statistics |
|
4 |
GEMINI windower |
Conducting analyses on genome "windows" |
|
4 |
Genbank to GFF3 |
converter |
|
2 |
genbank-to-genbank.gz |
converter |
|
1 |
genbank.gz-to-genbank |
converter |
|
1 |
Genbank2Fasta |
convert genbank format into fasta format |
|
1 |
Gene Align and Family Aggregator |
generates an SQLite database that can be visualised with Aequatus |
|
2 |
Gene BED To Exon/Intron/Codon BED |
expander |
|
1 |
Gene Body Coverage (BAM) |
Read coverage over gene body. |
|
13 |
Gene Body Coverage (Bigwig) |
Read coverage over gene body |
|
12 |
Gene Copy Number Finder |
from a genetree using the ETE Toolkit |
|
2 |
Gene length and GC content |
from GTF and FASTA file |
|
4 |
Gene prediction |
using GeneMarkSuites |
|
1 |
Gene prediction |
using glimmer3 |
|
1 |
Gene validation |
based on blastp and hmm analysis. |
|
1 |
Gene(translation) |
to amino acid seqs. |
|
1 |
gene2canonexons |
Extract exon coordinates of a Gene |
|
1 |
Gene2COG |
Gene annotation to cog using blastp |
|
1 |
Gene2Gene |
is analysis to find out genes presented in common geneme(NCBIRef). |
|
1 |
Gene2Pathway |
summary gene list to pathway. |
|
1 |
Gene2Pathway |
summary gene list to pathway. |
|
1 |
GeneFamilyAligner |
aligns integrated orthologous gene family clusters |
|
1 |
GeneFamilyClassifier |
classifies gene sequences into pre-computed orthologous gene family clusters |
|
2 |
GeneFamilyIntegrator |
integrates gene models in pre-computed orthologous gene family clusters with classified gene coding sequences |
|
2 |
GeneFamilyPhylogenyBuilder |
builds phylogenetic trees of aligned orthologous gene family clusters |
|
2 |
Geneid2Description |
assign gene description to data frame. |
|
1 |
GeneNetwork |
by distance or correlations. |
|
1 |
GenePhys |
Extract the genes underlying a genetic segment defined by genetic markers |
|
1 |
Generalized linear models |
for classification and regression |
|
11 |
Generate |
random samples with controlled size and complexity |
|
12 |
Generate 6-frame translation |
Translates DNA/RNA to protein |
|
1 |
Generate A Matrix |
for using PC and LDA |
|
1 |
Generate all possible combination of STR length profile |
of the consecutive allele from given error profile |
|
1 |
Generate BED file |
for a list of genes |
|
1 |
Generate box-whisker |
plot of quality score distribution over positions in nanopore reads |
|
2 |
Generate conformers |
using RDKit |
|
2 |
Generate gene to transcript map |
for Trinity assembly |
|
10 |
Generate heatmap |
with hierarchical clustering of both samplesand microbial clades for MetaPhlAn2 |
|
2 |
Generate histogram |
of nanopore read lengths |
|
2 |
Generate MD topologies for small molecules |
using acpype |
|
9 |
generate mock from frequencies and test repertoire |
generate mock from frequencies and test repertoire |
|
1 |
Generate pileup |
from BAM dataset |
|
3 |
Generate simulated reads |
from a fasta sequence using dwgsim |
|
1 |
Generate SuperTranscripts |
from a Trinity assembly |
|
6 |
Generating |
Barcode primers |
|
1 |
Generation, personalization and annotation of tree |
for GraPhlAn |
|
2 |
Generic_Filter |
Removes elements according to numerical or qualitative values |
|
3 |
GeneSeqToFamily preparation |
converts data for the workflow |
|
4 |
GeneTrack |
peak predictor |
|
2 |
genform |
Generation of molecular formulas by high-resolution MS and MS/MS data |
|
1 |
GenoCopy |
import a file or directory from your Genocluster worspace to the current history |
|
1 |
GenoLink |
imports file from your GenOuest workspace to the current history WITHOUT copying |
|
1 |
Genome annotation statistics |
|
|
1 |
Genome plot |
using genoPlotR |
|
1 |
GenomeScope |
reference-free genome profiling |
|
3 |
GenomicSuperSignature |
interpretation of RNAseq experiments |
|
1 |
GenoSend |
export history files to your GenOuest workspace |
|
1 |
Genrich |
Detecting sites of genomic enrichment |
|
3 |
Get Amplicon GC-Content |
|
|
1 |
Get climatic data from Worldclim |
|
|
1 |
Get Codon and Bicodon frequency |
from FASTA files |
Coding region prediction
Codon usage analysis
Codon usage table generation
Genome annotation
|
1 |
Get Codon frequency |
from bicodons |
Coding region prediction
Codon usage analysis
Codon usage table generation
Genome annotation
|
1 |
Get features by Ensembl ID |
using REST API |
|
3 |
Get flanks |
returns flanking region/s for every gene |
Sequence analysis
|
4 |
Get gene tree by Ensembl ID |
using REST API |
|
4 |
Get homopolymer run length |
Annotate indel variants with homopolymer context |
|
1 |
Get longest read |
from a set of FAST5 files. |
|
2 |
Get Microbial Data |
|
Query and retrieval
|
1 |
Get motifs from AREsite2 |
AREsite2 REST Interface |
|
1 |
Get open reading frames (ORFs) or coding sequences (CDSs) |
e.g. to get peptides from ESTs |
|
5 |
Get Pathways |
: Look up KEGG pathways for given Ensembl transcripts |
|
2 |
Get PDB file |
from Protein Data Bank |
|
2 |
Get peaklists |
or an average peaklist from a Peak Intensity Matrix |
|
2 |
Get RT Stop Counts |
derives the reverse transcriptase (RT) stop count on each nucleotide from a mapped file provided by the Iterative Mapping module |
|
1 |
Get Sentences |
from Sentences lines with words/phase |
|
1 |
Get Sequence |
from NCBI GenBank |
|
1 |
Get sequences by Ensembl ID |
using REST API |
|
3 |
Get Similar sentences |
from a data bases(ghostwriter----based on ChenChenMatrix) |
|
1 |
Get species occurrences data |
from GBIF, ALA, iNAT and others |
|
1 |
Get.communitytype |
description |
|
5 |
Get.coremicrobiome |
fraction of OTUs for samples or abundances |
|
6 |
Get.dists |
selects distances from a phylip or column file |
|
5 |
Get.group |
group names from shared or from list and group |
|
6 |
Get.groups |
Select groups |
|
5 |
Get.label |
label names from list, sabund, or rabund file |
|
5 |
Get.lineage |
Picks by taxon |
|
6 |
Get.mimarkspackage |
creates a mimarks package form with your groups |
|
5 |
Get.otulabels |
Selects OTU labels |
|
6 |
Get.otulist |
Get otus for each distance in a otu list |
|
5 |
Get.oturep |
Generate a fasta with a representative sequence for each OTU |
|
5 |
Get.otus |
Get otus containing sequences from specified groups |
|
5 |
Get.rabund |
Get rabund from a otu list or sabund |
|
6 |
Get.relabund |
Calculate the relative abundance of each otu |
|
5 |
Get.sabund |
Get sabund from a otu list or rabund |
|
5 |
Get.seqs |
Picks sequences by name |
|
5 |
Get.sharedseqs |
Get shared sequences at each distance from list and group |
|
5 |
Get_16S_rRNA |
reference sequecnes of a fasta query file |
|
1 |
Get_Seqs |
by ids. |
|
1 |
GetFastaBed |
use intervals to extract sequences from a FASTA file |
|
20 |
GetOneWayExperimentDesign |
Based on Sample names and Defined levels of Factors. |
|
1 |
getorf |
Finds and extracts open reading frames (ORFs) |
|
5 |
GetRange |
get the ranges for the dataframe |
|
1 |
getStacks |
get Stacks |
|
1 |
GetWithinDist |
using pairwise distance and seq2otu assignment. |
|
1 |
GFA to FASTA |
Convert Graphical Fragment Assembly files to FASTA format |
|
4 |
gfastats |
the swiss army knife for genome assembly |
|
8 |
GFF-to-BED |
converter |
|
2 |
GFF-to-BED |
converter |
Conversion
|
1 |
GFF-to-GTF |
converter |
|
1 |
GFF3 to Apollo Annotations |
|
|
8 |
gff3.bz2-to-gff3 |
converter |
|
1 |
GFF3_to_GTF |
converter |
|
1 |
GffCompare |
compare assembled transcripts to a reference annotation |
|
5 |
gffread |
Filters and/or converts GFF3/GTF2 records |
|
7 |
GIANT-Differential Expression with LIMMA |
Use LIMMA to detect differentially expressed genes |
|
2 |
GIANT-Factor file generator |
Generate factor file used by other GIANT tools |
|
2 |
GIANT-GSEA Formating |
Format input files for GSEA software |
|
2 |
GIANT-Heatmap and Hierarchical clustering |
Run hierarchical clustering and plot heatmap from expression data and/or differential expression analysis |
|
2 |
GIANT-Normalization with APT Summarize |
Apply Affymetrix Power Tool summarize function to .CEL collection |
|
2 |
GIANT-Plot volcanos |
Plot volcano from tabular file |
|
2 |
GIANT-QC Plots |
Descriptive plots of .CEL collections or normalized expression data |
|
2 |
Glimmer ICM builder |
|
|
1 |
Glimmer ICM builder |
|
|
1 |
Glimmer3 |
Predict ORFs in prokaryotic genomes (knowlegde-based) |
|
1 |
Glimmer3 |
Predict ORFs in prokaryotic genomes (not knowlegde-based) |
|
1 |
Glimmer3 |
Predict ORFs in prokaryotic genomes (not knowlegde-based) |
|
1 |
Glimmer3 |
Predict ORFs in prokaryotic genomes (knowlegde-based) |
|
1 |
glint_align |
align a genomic sequence against a whole genome |
|
1 |
GMAJ |
Multiple Alignment Viewer |
|
1 |
GMAP |
align the DNA sequence to reference genome |
|
1 |
GOAnnotator |
Accesses information from the Gene Ontology |
|
1 |
GOEnricher |
Compute Gene Set Enrichment Analysis |
|
1 |
GOEnrichment |
performs GO enrichment analysis of a set of gene products |
|
2 |
GOFunSim |
Compute similarity between pairs of proteins |
|
1 |
Golm Metabolome Database search spectrum |
: GC-MS Mass Spectral Database. |
|
2 |
goseq |
tests for overrepresented gene categories |
Gene-set enrichment analysis
|
12 |
GOSlimmer |
converts a set of annotation from GO to a given GOSlim version |
|
2 |
GotohScan |
Find subsequences in db |
|
2 |
GPASS |
significant single-SNP associations in case-control studies |
|
1 |
gProfiler Convert |
converts between various types of namespaces |
|
2 |
gProfiler GOSt |
performs functional enrichment analysis of gene lists |
Gene-set enrichment analysis
|
2 |
gProfiler Orth |
translates gene identifiers between organisms |
|
2 |
gProfiler Random |
generates a gene list |
|
2 |
gProfiler SNPense |
maps SNP rs-codes to gene names, chromosomal coordinates and variant effects |
|
2 |
Graphclust glob_report collect clusters |
|
|
1 |
GraphEmbed |
Compute and plot a 2D embedding of a data matrix given supervised class information |
|
1 |
grapher |
- displays results from Smilefinder |
|
1 |
GraPhlAn |
to produce graphical output of an input tree |
|
2 |
GraphProt |
- Train models and predict RBP binding profiles |
|
3 |
GrayToColor |
take grayscale images and produces a color image from them |
|
2 |
gro-to-pdb |
converter |
|
1 |
GROMACS copy file |
from built-in datasets |
|
2 |
GROMACS energy minimization |
of the system prior to equilibration and production MD |
|
7 |
GROMACS initial setup |
of topology and GRO structure file |
|
6 |
GROMACS production simulation |
for data collection |
|
2 |
GROMACS Radius of Gyration |
of a molecular structure |
|
2 |
GROMACS simulation |
for system equilibration or data collection |
|
9 |
GROMACS solvation and adding ions |
to structure and topology files |
|
8 |
GROMACS structure configuration |
using editconf |
|
5 |
Group |
data by a column and perform aggregate operation on other columns. |
|
4 |
Group abundances |
of UniRef50 gene families obtained (HUMAnN2 output) to Gene Ontology (GO) slim terms |
|
2 |
GTF-to-BEDGraph |
converter |
Conversion
|
1 |
GTF-to-GFF |
converter |
|
1 |
gtf-to-interval_index |
converter |
|
1 |
GTF2GeneList |
extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer |
|
6 |
GTF_to_GFF3 |
converter |
|
1 |
Gubbins |
Recombination detection in Bacteria |
|
2 |
Gumbel |
- determine essential genes |
|
6 |
Hammock - cluster peptides |
Clusters short peptide sequences |
|
5 |
hamronize |
parse multiple Antimicrobial Resistance Analysis Reports into a common data structure |
|
3 |
hamronize: summarize |
harmorization reports |
|
4 |
Haplotype Caller |
Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region |
|
3 |
Hardklor |
identification of features from mass spectra |
|
4 |
Hcluster |
Assign sequences to OTUs (Operational Taxonomic Unit) |
|
2 |
hcluster_sg |
Hierarchically clustering on a sparse graph |
|
2 |
hcluster_sg parser |
converts hcluster_sg 3-column output into lists of IDs |
|
4 |
Heatmap |
Heatmap of the dataMatrix |
|
2 |
Heatmap |
of numeric data |
|
1 |
Heatmap w ggplot |
|
|
6 |
Heatmap.bin |
Generate a heatmap for OTUs |
|
5 |
Heatmap.sim |
Generate a heatmap for pariwise similarity |
|
5 |
heatmap2 |
|
|
6 |
Heatmap2 |
analysis |
|
1 |
helixturnhelix |
Report nucleic acid binding motifs |
|
5 |
Hexamer frequency |
calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences |
|
6 |
HHsearch |
detecting remote homologues of proteins |
|
1 |
hicAdjustMatrix |
adjust the shape of a Hi-C matrix |
|
6 |
hicAggregateContacts |
allow plotting of aggregated Hi-C contacts between regions specified in a file |
|
10 |
hicAverageRegions |
sums Hi-C contacts around given reference points and computes their average. |
|
6 |
hicBuildMatrix |
create a contact matrix |
|
18 |
hicCompareMatrices |
normalize and compare two Hi-C contact matrices |
|
11 |
hicCompartmentalization |
compute pairwise correlations between multiple Hi-C contact matrices |
|
6 |
hicConvertFormat |
Convert between different file formats |
|
7 |
hicCorrectMatrix |
run a Hi-C matrix correction algorithm |
|
17 |
hicCorrelate |
compute pairwise correlations between multiple Hi-C contact matrices |
|
15 |
hicDetectLoops |
searches for enriched regions |
|
6 |
hicDifferentialTAD |
searches for differential TADs |
|
2 |
hicFindRestSite |
identify restriction enzyme sites |
|
7 |
hicFindTADs |
identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin |
|
16 |
hicHyperoptDetectLoops |
optimizes parameters for hicDetectLoops |
|
2 |
hicInfo |
get information about the content of a Hi-C matrix |
|
6 |
hicMergeDomains |
Merges TAD domains |
|
2 |
hicMergeLoops |
merge detected loops of different resolutions. |
|
7 |
hicMergeMatrixBins |
merge adjacent bins from a Hi-C contact matrix to reduce its resolution |
|
15 |
hicNormalize |
normalizes a matrix to norm range or smallest read count |
|
7 |
hicPCA |
compute the principal components for A / B compartment analysis |
|
12 |
hicPlotAverageRegions |
plot the average regions from hicAverageRegions |
|
7 |
hicPlotDistVsCounts |
compute distance vs Hi-C counts plot per chromosome |
|
15 |
hicPlotMatrix |
plot a Hi-C contact matrix heatmap |
|
16 |
hicPlotSVL |
plots the relation of short vs long range contacts |
|
6 |
hicPlotTADs |
plot Hi-C contact matrices heatmaps alongside other data tracks |
|
9 |
hicPlotViewpoint |
plot interactions around a viewpoint |
|
12 |
hicQuickQC |
get a first quality estimate of Hi-C data |
|
7 |
hicSumMatrices |
combine Hi-C matrices of the same size |
|
16 |
hicTransform |
transform a matrix to obs/exp, pearson and covariance matrices |
|
12 |
Hicup Deduplicator |
removes duplicated di-tags (retaining one copy of each) from the data set. |
|
4 |
Hicup Digester |
cuts throughout a selected genome at one or two specified restriction sites. |
|
4 |
Hicup Filter |
classifies read pairs, identifying valid Hi-C di-tags |
|
4 |
Hicup Mapper |
aligns paired reads independently to a reference genome and retains reads where both partners align. |
|
4 |
Hicup Pipeline |
controls the other programs in the HiCUP pipeline. |
|
4 |
Hicup to juicer converter |
|
|
1 |
Hicup Truncater |
terminates sequence reads at specified Hi-C ligation junctions. |
|
4 |
hicValidateLocations |
validate detected loops with protein peaks. |
|
6 |
Hierarchical clustering |
from MD RMSD matrix data |
|
3 |
Hifiasm |
haplotype-resolved de novo assembler for PacBio Hifi reads |
|
11 |
hifive |
manipulate, analyze, and plot HiC and 5C chromatin interaction data |
|
2 |
HISAT2 |
A fast and sensitive alignment program |
|
19 |
Histogram |
of a numeric column |
|
4 |
Histogram equalization |
automatic histogram equalization |
|
1 |
Histogram w ggplot2 |
|
|
7 |
HistPairWiseDistance |
describle the distribution of pairwise distance. |
|
1 |
HMDB MS search |
search by masses on HMDB online LCMS bank |
|
6 |
HMM |
- determine essentiality of a genome |
|
6 |
hmmalign |
align sequences to a profile HMM |
|
7 |
hmmbuild |
Build a profile HMM from an input multiple alignment |
|
8 |
hmmconvert |
convert profile file to a HMMER format |
|
7 |
hmmemit |
sample sequence(s) from a profile HMM |
|
7 |
hmmfetch |
retrieve profile HMM(s) from a file |
|
7 |
hmmscan |
search sequence(s) against a profile database |
|
8 |
hmmsearch |
search profile(s) against a sequence database |
|
8 |
hmoment |
Hydrophobic moment calculation |
|
5 |
Homology Classifier and Filter |
from a genetree using the ETE Toolkit |
|
4 |
Homoscedasticity and normality |
Checks the homogeneity of the variance and the normality of the distribution |
|
1 |
Homova |
Homogeneity of molecular variance |
|
5 |
Homozygosity Mapping |
Create Homozygosity Map using Plink |
|
1 |
HorizBarplot |
of pathway enrichemnt analysis. |
|
1 |
HSEnsg2gcoords |
Assign gene borders for Ensembl gene IDs. |
|
1 |
HSEnsgProteinMapper |
Maps between a variety of protein IDs for H.sapiens |
|
1 |
HSGeneAtlas |
GNF Gene Atlas gene expression data supplementing for H.sapiens |
|
1 |
HSGeneIdConverter |
H.sapiens gene ID conversion |
|
1 |
HSGeneOrthologyMapper |
Orthology mapping for H.sapiens |
|
1 |
HTSeq Coverage |
calculator of sam files |
|
1 |
htseq-count |
- Count aligned reads in a BAM file that overlap features in a GFF file |
|
9 |
HugoEnsmbl |
Convert HUGO 2 ENSEMBL |
|
1 |
HUMAnN |
to profile presence/absence and abundance of microbial pathways and gene families |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
HUMAnN2 |
to profile presence/absence and abundance of microbial pathways and gene families |
|
5 |
HVIS |
visualization of genomic data with the Hilbert curve |
|
2 |
Hydrogen Bond Analysis |
- analyze H-bonds between two segments |
|
4 |
Hydrogen Bond Analysis using VMD |
between two segments of a trajectory |
|
1 |
Hyperparameter Search |
performs hyperparameter optimization using various SearchCVs |
|
11 |
HyPhy-aBSREL |
adaptive Branch Site Random Effects Likelihood |
|
27 |
HyPhy-BGM |
- Detecting coevolving sites via Bayesian graphical models |
|
26 |
HyPhy-BUSTED |
Branch-site Unrestricted Statistical Test for Episodic Diversification |
|
26 |
HyPhy-CFEL |
Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches |
|
6 |
HyPhy-Conv |
translate an in-frame codon alignment to proteins |
|
5 |
HyPhy-FADE |
: FUBAR* Approach to Directional Evolution (*Fast Unconstrained Bayesian Approximation) |
|
25 |
HyPhy-FEL |
Fixed Effects Likelihood |
|
25 |
HyPhy-FUBAR |
Fast Unconstrained Bayesian AppRoximation |
|
25 |
HyPhy-GARD |
Genetic Algorithm for Recombination Detection |
|
26 |
HyPhy-MEME |
Mixed Effects Model of Evolution |
|
25 |
HyPhy-PRIME |
Property Informed Models of Evolution |
|
20 |
HyPhy-RELAX |
Detect relaxed selection in a codon-based phylogenetic framework |
|
24 |
HyPhy-SLAC |
Single Likelihood Ancestor Counting |
|
25 |
HyPhy-SM2019 |
Partition Tree using Modified Slatkin-Maddison Test |
|
24 |
HyPhy-Summary |
generate summary report of HyPhy analyses |
|
6 |
IC50 Filter: |
Select neoepitopes based on predicted IC50 |
|
1 |
ID choice |
Choosing a particular column in your metadata to be considered as Identifiers |
|
2 |
ID Filter |
apply filter to ids |
|
1 |
IDBA-HYBRID |
Iterative de Bruijn Graph Assembler for hybrid sequencing data |
|
2 |
IDBA-TRAN |
Iterative de Bruijn Graph Assembler for transcriptome data |
|
3 |
IDBA-UD |
Iterative de Bruijn Graph Assembler for data with highly uneven depth |
|
3 |
idconvert |
Convert mass spectrometry identification files |
|
4 |
Identification Parameters |
Sets the identification parameters to be used in SearchGUI and PeptideShaker apps |
|
6 |
Identify optimal scoring subnetwork |
using Heinz |
|
2 |
IdentifyPrimaryObjects |
identify biological objects of interest |
|
2 |
idpAssemble |
Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels. |
|
4 |
idpEmbedder |
Embed human/mouse gene metadata into IDPicker files |
|
4 |
idpQonvert |
Prepare identification results for IDPicker |
|
4 |
idpQuery |
Creates text reports from idpDB files. |
|
5 |
IDR |
compare ranked list of identifications |
|
2 |
IDR/OMERO Download |
- download images from any OMERO instance using image IDs |
|
10 |
IdxStats |
reports stats of the BAM index file |
|
8 |
IEDB |
MHC Binding prediction |
|
3 |
iep |
Calculates the isoelectric point of a protein |
|
5 |
Illuminapairedend - Assembling pair-end reads |
Construct consensus reads from Illumina pair-end reads |
|
3 |
Image |
for plotting an image based on a dataframe. |
|
1 |
Image Converter |
|
|
3 |
Image Filmify |
Change image to funky film-frame looking image. |
|
1 |
Image Info |
Show Image Info |
|
2 |
Image Montage |
|
|
3 |
Image Registration |
based on intensity information |
|
3 |
Image Resize |
Resize the image. |
|
1 |
Image Rotate |
Rotate the image. |
|
1 |
Image Tileify |
Change image to funky tiled looking image. |
|
1 |
ImageMath |
perform simple mathematical operations on images |
|
2 |
ImageSplitDf |
split the statistic table for the image plot. |
|
1 |
Import Anndata and loom |
from different format |
|
9 |
Inbreeding and kinship |
: Analyze the pedigree without genomic data |
|
2 |
InChI to CML |
|
|
2 |
InChI to MOL2 |
|
|
2 |
InChI to SDF |
|
|
2 |
InChI to SMILES |
|
|
2 |
inchi-to-mol |
converter |
|
2 |
Indel Realigner |
- perform local realignment |
|
3 |
Indel Realigner |
- perform local realignment |
|
1 |
IndicativeNetwork |
indicates association of taxa with one or the other treatments. |
|
1 |
Indicator |
Identify indicator "species" for nodes on a tree |
|
5 |
Infer Experiment |
speculates how RNA-seq were configured |
|
12 |
Infinium Human Methylation BeadChip |
Determines differentially methylated regions and positions from Infinium Methylation Assays |
|
1 |
infoseq |
Displays some simple information about sequences |
|
5 |
Initial processing using RaceID |
performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data |
|
8 |
Inner Distance |
calculate the inner distance (or insert size) between two paired RNA reads |
|
12 |
input_peptides_and_regroup |
regroup peptides to fasta |
|
1 |
Insert indel qualities |
into a BAM file |
|
4 |
Insertion Profile |
calculates the distribution of inserted nucleotides across reads |
|
6 |
Insertion size metrics |
for PAIRED data |
|
3 |
Inspect and manipulate |
with scanpy |
|
7 |
Inspect AnnData |
object |
|
10 |
Inspect Expression Set Object |
Inspect an ExpressionSet object by a variety of attributes |
|
5 |
InStrain Compare |
Compares multiple inStrain profiles (popANI, coverage_overlap, etc.) |
Cross-assembly
Genome comparison
SNP detection
|
2 |
InStrain Profile |
Creates an inStrain profile (microdiversity analysis) from a mapping file |
Cross-assembly
Genome comparison
SNP detection
|
2 |
Intensity Check |
Statistical measures, number of missing values and mean fold change |
|
2 |
InteractionAnnotator |
Find interacting proteins with iRefIndex |
|
1 |
InterProScan |
functional annotation |
|
9 |
Intersect |
the intervals of two datasets |
Filtering
|
6 |
Intersect |
multiple VCF datasets |
|
2 |
Intersect |
Generate the intersection of two VCF files |
|
2 |
Intersect BAM alignments with intervals in another files |
|
|
2 |
Intersect intervals |
find overlapping intervals in various ways |
|
22 |
Interval2Genes |
Finds all genes contained in an interval. |
|
1 |
IQ-TREE |
Phylogenomic / evolutionary tree construction from multiple sequences |
|
7 |
iReport |
create an HTML report |
|
1 |
Iris |
Refine insertion sequences |
|
3 |
isochore |
Plots isochores in large DNA sequences |
|
5 |
IsoDE2 |
Computes differentially expressed isoforms and genes based on bootstrap samples generated by IsoEM2 |
|
1 |
IsoEM2 |
Infers isoform and gene expression levels with bootstrap based confidence intervals from either sense, antisense, or non-stranded RNA-Seq data |
|
1 |
Isoplot: Generate plots from isocor output |
|
|
2 |
Isotope Correction for mass spectrometry labeling experiments |
|
|
1 |
Iterative Mapping |
iteratively maps the raw reads of RNA structural data to the reference transcriptome |
|
1 |
iTraq4plex analysis via X-Tracker |
Execute iTraq4plex quantitation method via X-Tracker |
|
1 |
ITSx |
identifies ITS sequences and extracts the ITS region |
|
1 |
IUPAC name-to-structure |
converter (OPSIN) |
|
1 |
ivar consensus |
Call consensus from aligned BAM file |
|
9 |
ivar filtervariants |
Filter variants across replicates or multiple samples aligned using the same reference |
|
7 |
ivar getmasked |
Detect primer mismatches and get primer indices for the amplicon to be masked |
|
4 |
ivar removereads |
Remove reads from trimmed BAM file |
|
11 |
ivar trim |
Trim reads in aligned BAM |
|
13 |
ivar variants |
Call variants from aligned BAM file |
|
9 |
IWTomics Load |
Smooth and Plot |
|
1 |
IWTomics Plot with Threshold |
on Test Scale |
|
1 |
IWTomics Test |
and Plot |
|
1 |
jackhmmer |
iteratively search a protein sequence against a protein database (PSIBLAST-like) |
|
8 |
JasmineSV |
Merge structural variants across samples |
|
2 |
JBrowse |
genome browser |
Map drawing
Sequence visualisation
|
31 |
JBrowse - Data Directory to Standalone |
upgrades the bare data directory to a full JBrowse instance |
Conversion
|
30 |
Je-Clip |
clips Unique Molecular Identifiers (UMIs) from fastq files |
|
2 |
Je-Demultiplex |
demultiplexes fastq files |
|
2 |
Je-Demultiplex-Illu |
demultiplexes fastq files using Illumina Index file |
|
2 |
Je-MarkDuplicates |
to filter BAM files for read duplicates taking UMIs into account |
|
2 |
jellyfish |
|
|
1 |
Join |
the intervals of two datasets side-by-side |
Aggregation
|
5 |
Join |
two files |
|
12 |
Join |
HUMAnN2 generated tables |
|
4 |
Join (merge) |
gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Join +/- Ions |
Join positive and negative ionization-mode W4M datasets for the same samples |
|
1 |
Join MAF blocks |
by Species |
|
1 |
Join neighbors |
rapidly with RapidNJ |
|
1 |
Join two Datasets |
side by side on a specified field |
|
4 |
Join two files |
on column allowing a small difference |
|
2 |
JQ |
process JSON |
|
1 |
Junction Annotation |
compares detected splice junctions to reference gene model |
|
12 |
Junction Saturation |
detects splice junctions from each subset and compares them to reference gene model |
|
12 |
KaKsAnalysis |
estimates paralogous and orthologous pairwise synonymous (Ks) and non-synonymous (Ka) substitution rates |
|
1 |
Kallisto pseudo |
- run pseudoalignment on RNA-Seq transcripts |
|
6 |
Kallisto quant |
- quantify abundances of RNA-Seq transcripts |
|
8 |
Karyotype Plotting tool |
for multiple series |
|
1 |
Kc-Align |
|
|
11 |
KEGGMapGeneAbundance |
calculate the geneabundance for KEGG pathways(Shotgun metagnomics). |
|
1 |
Kernel Canonical Correlation Analysis |
|
|
2 |
Kernel Principal Component Analysis |
|
|
2 |
khmer: Abundance Distribution |
Calculate abundance distribution of k-mers using pre-made k-mer countgraphs |
|
4 |
khmer: Abundance Distribution (all-in-one) |
Calculate abundance distribution of k-mers |
|
4 |
khmer: Count Median |
Count the median/avg k-mer abundance for each sequence |
|
4 |
khmer: Extract partitions |
Separate sequences that are annotated with partitions into grouped files |
|
4 |
khmer: Filter reads |
by minimal k-mer abundance |
|
4 |
khmer: Filter reads |
below k-mer abundance of 50 |
|
4 |
khmer: Normalize By Median |
Filter reads using digital normalization via k-mer abundances |
Sequence file editing
Sequence word comparison
|
5 |
khmer: Sequence partition all-in-one |
Load, partition, and annotate sequences |
|
4 |
KING |
Kinship-based INference for GWAS |
|
2 |
Kinwalker |
cotranscriptional folding of RNAs |
|
1 |
KisSplice |
is a local transcriptome assembler for SNPs, indels and AS events |
|
3 |
Kmer Cluster |
analyses and plot |
|
1 |
KmerFreq AR |
- a kmer frequency counter |
|
1 |
KmerFreq HA |
- a kmer frequency counter |
|
1 |
KmerFreq1 |
- a kmer frequency counter |
|
1 |
KO2Modules |
map KEGG module based on KOs |
|
1 |
KOBAS Annotate |
KEGG Orthology Based Annotation System |
|
3 |
KOBAS Identify |
KEGG Orthology Based Annotation System |
|
3 |
KOFamScan |
基于KEGG的kofamscan注释基因(氨基酸序列)。Annotating AA sequences to KEGG KO using kofamscan. |
|
1 |
KofamScan |
gene function annotation based on KEGG orthology and HMM |
|
2 |
Kraken |
assign taxonomic labels to sequencing reads |
|
8 |
Kraken taxonomic report |
view report of classification for multiple samples |
|
3 |
Kraken-filter |
filter classification by confidence score |
|
4 |
Kraken-mpa-report |
view report of classification for multiple samples |
|
5 |
Kraken-report |
view sample report of a classification |
|
5 |
Kraken-translate |
convert taxonomy IDs to names |
|
4 |
Kraken2 |
assign taxonomic labels to sequencing reads |
|
5 |
Krona pie chart |
from taxonomic profile |
|
10 |
Kronik |
processes Hardklor features to find peptides by chromatographic profiling |
|
4 |
KsDistribution |
plots the distribution of synonymous substitution (Ks) rates and fits significant component(s) |
|
1 |
Label free protein |
summarisation and quantitation |
|
1 |
Label to Points |
Converts label image to points |
|
2 |
LAJ |
Pairwise Alignment Viewer |
|
1 |
Landmark Registration |
using least squares |
|
2 |
Landmark Registration |
Landmark Registration |
|
5 |
LAST-split |
finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). |
|
4 |
LAST-train |
finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. |
|
5 |
LASTal |
finds local alignments between query sequences, and reference sequences. |
|
6 |
LASTdb |
prepares sequences for subsequent comparison and alignment using lastal. |
|
5 |
LASTZ |
: align long sequences |
|
7 |
Lastz paired reads |
map short paired reads against reference sequence |
|
2 |
LASTZ_D |
: estimate substitution scores matrix |
|
5 |
LAV to BED |
Converts a LAV formatted file to BED format |
|
1 |
LCMS matching |
Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. |
|
3 |
LD |
linkage disequilibrium and tag SNPs |
|
1 |
Lefse |
description |
|
5 |
legsta |
Legionella pneumophila sequence based typing |
|
2 |
Length Distribution |
chart |
|
2 |
LibCompare |
statistic analysis for library comparison. |
|
1 |
LibCompareFolds |
statistic analysis usng the algorithm describled in RDP libcompare. |
|
1 |
LibCompareTab |
statistic analysis usng the algorithm describled in RDP libcompare. |
|
1 |
Libshuff |
Cramer-von Mises tests communities for the same structure |
|
5 |
liftgcoords |
Lifts Genomic Coordinates from any build to the most recent |
|
1 |
lighter |
can correct the reads containing sequence errors |
|
1 |
LightGBM |
- train and apply LightGBM models |
|
3 |
limma |
Perform differential expression with limma-voom or limma-trend |
Differential gene expression profiling
RNA-seq read count analysis
|
19 |
lindna |
Draws linear maps of DNA constructs |
|
5 |
Line/Word/Character count |
of a dataset |
|
1 |
Lineage Branch Analysis using StemID |
inspects branches of a lineage tree |
|
6 |
Lineage computation using StemID |
generates lineage from prior clustering |
|
6 |
Linear regression ajusted |
for autocorrelation in the residuals |
|
1 |
Linear regression ajusted |
for autocorrelation in the residuals |
|
1 |
LINKS |
- scaffold genome assemblies with long reads |
|
1 |
Lipidmaps |
: search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. |
|
1 |
List |
genes in pathway of a KEGG organisms(www.kegg.jp) |
|
1 |
List Organisms |
in Apollo |
|
8 |
List spaln parameter tables |
Given a query species, list the spaln settings tables that exist, from closest related species to most different |
|
4 |
List.otulabels |
Lists otu labels from shared or relabund file |
|
5 |
List.seqs |
Lists the names (accnos) of the sequences |
|
5 |
List2Table |
convert a 2column lists into 2D table |
|
1 |
listfiltering |
Compare list1 and list2 |
|
1 |
ListSamples |
in a data frame |
|
1 |
Load Abstract |
into database(Only for developping team) |
|
1 |
Load Article |
into database(Only for developping team) |
|
1 |
Load Sentence |
into database(Only for developping team) |
|
1 |
Local Contributions to Beta Diversity (LCBD) |
Computes a measure of beta diversity, SCBD and representations |
|
1 |
Local Threshold |
applies a local threshold algorithm to an image |
|
2 |
LocARNA |
Multiple Alignment and Folding of RNAs |
|
1 |
LocARNA Multiple Aligner |
Multiple Alignment and Folding of RNAs (mlocarna) |
|
2 |
locarna_graphclust |
|
|
3 |
Lofreq filter |
called variants posteriorly |
|
4 |
Logol |
Biological patterns matching |
|
1 |
Lordec |
is a set a programs for correcting sequencing errors in PacBio reads |
|
5 |
lorikeet spoligotyping |
M. tuberculosis DNA fingerprinting |
|
1 |
LotuS2 |
fast OTU processing pipeline |
|
10 |
LPS |
LASSO-Patternsearch algorithm |
|
1 |
LUMPY |
is a probabilistic framework for structural variant discovery |
|
2 |
LUMPY preprocessing |
extracts discordant read pairs and split-read alignments from a BAM dataset |
|
2 |
Machine Learning Visualization Extension |
includes several types of plotting for machine learning |
|
6 |
MACS |
Model-based Analysis of ChIP-Seq |
|
4 |
MACS2 |
Model-based Analysis of ChIP-Seq |
|
1 |
MACS2 bdgbroadcall |
Call broad peaks from bedGraph output |
|
9 |
MACS2 bdgcmp |
Deduct noise by comparing two signal tracks in bedGraph |
|
9 |
MACS2 bdgdiff |
Differential peak detection based on paired four bedgraph files |
|
10 |
MACS2 bdgpeakcall |
Call peaks from bedGraph output |
|
9 |
MACS2 callpeak |
Call peaks from alignment results |
|
12 |
MACS2 filterdup |
Remove duplicate reads at the same position |
|
9 |
MACS2 predictd |
Predict 'd' or fragment size from alignment results |
|
9 |
MACS2 randsample |
Randomly sample number or percentage of total reads |
|
9 |
MACS2 refinepeak |
Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) |
|
9 |
MAF boxplot |
Minor Allele Frequency Boxplot |
|
1 |
MAF Coverage Stats |
Alignment coverage information |
|
3 |
MAF to BED |
Converts a MAF formatted file to the BED format |
|
1 |
MAF to FASTA |
Converts a MAF formatted file to FASTA format |
|
1 |
MAF to Interval |
Converts a MAF formatted file to the Interval format |
|
1 |
MAF-convert |
read MAF-format alignments and write them in another format. |
|
4 |
MAFFT |
Multiple alignment program for amino acid or nucleotide sequences |
|
9 |
MAFFT add |
Align a sequence,alignment or fragments to an existing alignment. |
|
6 |
Magic-BLAST: map large RNA or DNA sequences |
against a whole genome or transcriptome |
|
3 |
Mahotas-features |
Compute features using mahotas |
|
1 |
Make Design |
Assign groups to Sets |
|
5 |
Make File |
: Build a gd_snp or gd_genotype file |
|
2 |
Make strain profiles |
|
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Make strain profiles |
|
|
3 |
Make Table |
based on denove OTU picking |
|
1 |
Make windows |
|
|
2 |
Make.biom |
Make biom files from a shared file |
|
5 |
Make.contigs |
Aligns paired forward and reverse fastq files to contigs as fasta and quality |
|
6 |
Make.fastq |
Convert fasta and quality to fastq |
|
6 |
Make.group |
Make a group file |
|
6 |
Make.lefse |
create a lefse formatted input file from mothur's output files |
|
6 |
Make.lookup |
allows you to create custom lookup files for use with shhh.flows |
|
5 |
Make.shared |
Make a shared file from a list and a group |
|
5 |
Make.sra |
creates the necessary files for a NCBI submission |
|
5 |
Make_Contig |
using pairwise alignment(We trust the begining of forward or reverse sequences). |
|
1 |
Maker |
genome annotation pipeline |
|
10 |
MALDIquant peak detection |
Peak detection, binning and filtering for mass-spectrometry imaging data |
|
7 |
MALDIquant preprocessing |
Preprocessing of mass-spectrometry imaging data |
|
4 |
MALT analyzer |
|
|
2 |
Manipulate AnnData |
object |
|
10 |
Manipulate Expression Set Object |
Manipulate ExpressionSet objects by a variety of attributes |
|
1 |
Manipulate FASTQ |
reads on various attributes |
Sequence conversion
|
4 |
Manipulate loom object |
Add layers, or row/column attributes to a loom file |
|
7 |
Manipulation |
of text lines with regular expressions (sed) |
|
1 |
Mantel |
Mantel correlation coefficient between two matrices. |
|
5 |
Mantel |
tests between two distant matrix or dataframe. |
|
1 |
Mantel tests |
不同环境变量对种群结构的解释能力. |
|
1 |
Map annotation ids |
on a Maker annotation |
|
5 |
Map peptides to a bed file |
for viewing in a genome browser |
|
3 |
map plot |
gridded (lat/lon) netCDF data |
|
2 |
Map Reads to OTU |
Maps read sequences to OTUs |
|
1 |
Map repertoire |
Map test repertoire |
|
1 |
Map Seqs |
between database |
|
1 |
Map with BFAST |
|
|
1 |
Map with Bowtie for Illumina |
|
|
7 |
Map with BWA |
- map short reads (< 100 bp) against reference genome |
|
12 |
Map with BWA for Illumina |
|
|
1 |
Map with BWA for SOLiD |
|
|
1 |
Map with BWA for STACKS |
from zip file with fastqsanger files |
|
1 |
Map with BWA-MEM |
- map medium and long reads (> 100 bp) against reference genome |
DNA mapping
Genetic mapping
Genome annotation
Mapping
Mapping assembly
Protein SNP mapping
Sequence assembly
Sequence tag mapping
|
14 |
Map with KMA |
|
|
2 |
Map with minimap2 |
A fast pairwise aligner for genomic and spliced nucleotide sequences |
Sequence alignment
|
18 |
Map with Mosaik |
|
|
1 |
Map with PerM |
for SOLiD and Illumina |
|
1 |
MapBacterialPathogens |
detect potential bacterial pathogens 16S rRNA sequences. |
|
1 |
MapBed |
apply a function to a column for each overlapping interval |
|
21 |
Mapper |
for long, error-prone reads, like Nanopore ONT and PacBio |
|
1 |
Mapping |
short sequences against a database using BWA or Magic Blast |
|
1 |
MappingKEGGbyKOs |
color the KEGG pathway by KOs. |
|
1 |
mappings |
peptide mappings |
|
1 |
Mapsembler2 |
is a targeted assembly software |
|
3 |
Mark Duplicate reads |
|
|
3 |
MarkDuplicates |
examine aligned records in BAM datasets to locate duplicate molecules |
|
17 |
MarkDuplicatesWithMateCigar |
examine aligned records in BAM datasets to locate duplicate molecules |
|
16 |
MarkinChina |
Mark your sample points in the map of China |
|
1 |
marscan |
Finds MAR/SAR sites in nucleic sequences |
|
5 |
mash screen |
determines how well query sequences are contained within a pool of sequences |
|
3 |
mash sketch |
Create a reduced representation of a sequence or set of sequences, based on min-hashes |
|
1 |
maSigPro |
Significant Gene Expression Profile Differences in Time Course Gene Expression Data |
|
5 |
Mask CpG/non-CpG sites |
from MAF file |
|
1 |
maskfeat |
Mask off features of a sequence |
|
5 |
MaskImage |
hide portions of an image based on previously identified objects |
|
2 |
maskseq |
Mask off regions of a sequence |
|
5 |
MassBank spectrum searches |
: Search by pseudo-spectra on a High Quality Mass Spectral Database. |
|
1 |
MasterVar to pgSnp |
Convert from MasterVar to pgSnp format |
|
1 |
matcher |
Finds the best local alignments between two sequences |
|
5 |
Matings |
: Assignment of optimal breeding pairs |
|
2 |
matrix-visualization |
with sorting and clustering) |
|
1 |
Max SuCOS score |
- determine maximum SuCOS score of ligands against clustered fragment hits |
|
7 |
MaxBin2 |
clusters metagenomic contigs into bins |
|
4 |
MaxQuant |
|
Imputation
Protein quantification
Statistical calculation
|
17 |
MaxQuant (using mqpar.xml) |
|
Imputation
Protein quantification
Statistical calculation
|
9 |
MC:pred |
Predicts the potential for missed cleavage of tryptic bonds within protein sequences |
|
1 |
MDS Scatter Plot |
of molecule similarity |
|
1 |
MDTraj file converter |
- interconvert between MD trajectory file formats. |
|
5 |
MEA |
Predict MEA structures and compare structures of RNAs |
|
1 |
MeanQualityByCycle |
chart distribution of base qualities |
|
14 |
MeasureGranularity |
output spectra of size measurements of the textures |
|
2 |
MeasureImageAreaOccupied |
measure the area in an image occupied by objects |
|
2 |
MeasureImageIntensity |
measure several intensity features across an entire image |
|
2 |
MeasureImageQuality |
measure features that indicate image quality |
|
2 |
MeasureObjectIntensity |
measure several intensity features for identified objects |
|
2 |
MeasureObjectSizeShape |
measure area and shape features of identified objects |
|
2 |
MeasureTexture |
quantify the roughness and smoothness of the textures |
|
2 |
medaka consensus pipeline |
Assembly polishing via neural networks |
|
11 |
medaka consensus tool |
Assembly polishing via neural networks |
|
10 |
medaka variant pipeline |
via neural networks |
|
9 |
medaka variant tool |
decodes variant calls from medaka consensus output |
|
14 |
Megablast |
compare short reads against htgs, nt, and wgs databases |
|
2 |
Megahit |
make contig with megahits. |
|
1 |
MEGAHIT |
for metagenomics assembly |
|
7 |
megahit contig2fastg |
for converting MEGAHIT's contigs (.fa) to assembly graphs (.fastg) |
|
1 |
megamerger |
Merge two large overlapping nucleic acid sequences |
|
5 |
MEGAN Blast2LCA: apply LCA alignment |
to produce a taxonomic classification |
|
1 |
MEGAN: Extract reads |
by classification |
|
1 |
MEGAN: Generate a MEGAN rma6 file |
from a DIAMOND or MALT sam file |
|
2 |
MEGAN: Generate a MEGAN rma6 file |
from a DIAMOND daa file |
|
2 |
MEGAN: Generate RMA files |
from BLAST output |
|
2 |
MEGAN: Get information |
about a DIAMOND file |
|
1 |
MEGAN: meganize a DIAMOND file |
for use with MEGAN |
|
2 |
melt |
collapse combinations of variables:values to single lines |
|
1 |
MEME |
- Multiple EM for Motif Elicitation |
|
10 |
MEME psp-gen |
- perform discriminative motif discovery |
|
6 |
MEME-ChIP |
- motif discovery, enrichment analysis and clustering on large nucleotide datasets |
|
3 |
MendelianFilter |
Filter variants that do not comply with Mendelian inheritence |
|
1 |
meneco |
compute minimal completions to your draft network with reactions from a repair network |
|
1 |
Merge |
multiple VCF datasets |
|
2 |
Merge |
the overlapping intervals of a dataset |
Sequence merging
|
5 |
Merge |
files into one |
|
1 |
Merge |
MetaPhlAn abundance tables |
Nucleic acid sequence analysis
Phylogenetic analysis
|
8 |
Merge BAM Files |
merges BAM files together |
|
3 |
Merge BedGraph files |
|
|
3 |
Merge Columns |
together |
|
4 |
Merge Counts |
|
|
1 |
Merge GROMACS topologies |
and GRO files |
|
7 |
Merge matching reads |
into clusters with TN-93 |
|
3 |
Merge Neighbours in Label |
Merge Neighbours in Label Image |
|
2 |
Merge pair |
- merges a pair of corrected read libraries |
|
1 |
Merge peaklists |
produced by the tools 'Process scans (and SIM-Stitch)' or 'Replicate filter' |
|
1 |
Merge.count |
Merge count tables |
|
2 |
Merge.files |
Merge data |
|
5 |
Merge.groups |
Merge groups in a shared file |
|
5 |
Merge.sfffiles |
Merge SFF files |
|
5 |
Merge.taxsummary |
Merge tax.summary files |
|
6 |
MergeBamAlignment |
merge alignment data with additional info stored in an unmapped BAM dataset |
|
14 |
MergeBlastResults |
Parse Blast result (Tabular) to merge feature |
|
1 |
MergeLogFiles |
Merge multiple log files |
|
1 |
MergeMultiFile |
Merge multiple files |
|
1 |
merger |
Merge two overlapping nucleic acid sequences |
|
5 |
MergeSamFiles |
merges multiple SAM/BAM datasets into one |
|
14 |
MergeSamFiles |
Merge multiple SAM files |
|
1 |
Merqury |
evaluate the assembly quality |
Genome assembly
|
4 |
Meryl |
a genomic k-mer counter and sequence utility |
Genome assembly
|
8 |
MetaBAT2 |
metagenome binning |
|
3 |
MetaCompVenn |
map KEGG module based on KOs |
|
1 |
MetaEuk Easy Predict |
High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics |
|
3 |
MetaGeneAnnotator |
gene-finding program for prokaryote and phage (used by sixgill) |
|
1 |
MetaGeneMarkerS |
predict gene using the metagenomic models |
|
1 |
Metagenome Contributions |
|
|
1 |
metagenomeSeq Normalization |
Cumulative sum scaling |
|
1 |
MetaModuleSummary |
make a summary of module according to the gene and taxa |
|
1 |
metaMS.runGC |
GC-MS data preprocessing using metaMS package |
|
6 |
MetaNovo |
Produce targeted databases for mass spectrometry analysis. |
|
2 |
MetaPhlAn |
to profile the composition of microbial communities |
Nucleic acid sequence analysis
Phylogenetic analysis
|
7 |
MetaPhlAn to Krona |
Converter |
|
1 |
MetaPhlAn to PhyloXML |
converter |
|
1 |
MetaPhlAn2 |
to profile the composition of microbial communities |
|
2 |
metaplasmidSPAdes |
extract and assembly plasmids from metagenomic data |
|
6 |
MetaProteomeAnalyzer |
functional and taxonomic characterization of proteins |
|
2 |
metaQuantome: create samples file |
by specifying the experiment's groups and associated column names |
|
6 |
metaQuantome: database |
download the GO, EC, and NCBI databases |
|
6 |
metaQuantome: expand |
a set of functional or taxonomy annotations |
|
6 |
metaQuantome: filter |
for quality, redundancy, and sample coverage |
|
6 |
metaQuantome: stat |
differential analysis of functional expression and taxonomic abundance |
|
6 |
metaQuantome: visualize |
taxonomic analysis, functional analysis, and function-taxonomy analysis results |
|
6 |
MetaRanker |
Computes MetaRanker scores from multiple columns |
|
1 |
metaSPAdes |
metagenome assembler |
|
12 |
Metastats |
generate principle components plot data |
|
5 |
metaviralSPAdes |
extract and assembly viral genomes from metagenomic data |
|
6 |
MetFrag |
in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra |
|
3 |
MetFrag Vis |
Visualisation for MetFrag results |
|
1 |
MethylDackel |
A tool for processing bisulfite sequencing alignments |
Gene methylation analysis
|
7 |
methylKit |
DNA methylation analysis and annotation |
|
1 |
metilene |
calling differentially methylated regions from bisulfite sequencing data |
|
5 |
MiGMAP |
mapper for full-length T- and B-cell repertoire sequencing |
|
5 |
Mimarks.attributes |
Reads bioSample Attributes xml and generates source for get.mimarkspackage command |
|
5 |
MiModD Convert |
converts sequence data into different formats |
|
2 |
MiModD Coverage Statistics |
calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool |
|
2 |
MiModD Deletion Calling (for PE data) |
predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes |
|
2 |
MiModD Extract Variant Sites |
from a BCF file |
|
2 |
MiModD File Information |
provides summary reports for supported sequence data formats. |
|
3 |
MiModD NacreousMap |
maps phenotypically selected variants by multi-variant linkage analysis |
|
3 |
MiModD Read Alignment |
maps sequence reads to a reference genome using SNAP |
|
1 |
MiModD Rebase Sites |
from a VCF file |
|
3 |
MiModD Reheader |
takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file |
|
2 |
MiModD Report Variants |
in a human-friendly format that simplifies data exploration |
|
3 |
MiModD Run Annotation |
writes run metadata in SAM format for attaching it to sequenced reads data |
|
2 |
MiModD Sort |
takes a SAM/BAM dataset and generates a coordinate/name-sorted copy |
|
2 |
MiModD Variant Calling |
generates a BCF file of position-specific variant likelihoods and coverage information based on a reference sequence and reads aligned against it |
|
2 |
MiModD VCF Filter |
extracts lines from a vcf variant file based on field-specific filters |
|
3 |
MINE |
- Maximal Information-based Nonparametric Exploration |
|
2 |
Minia |
Short-read assembler based on a de Bruijn graph |
|
3 |
miniasm |
Ultrafast de novo assembly for long noisy reads |
|
7 |
Miniprot align |
align a protein sequence against a genome with affine gap penalty, splicing and frameshift |
|
2 |
Miniprot index |
build a genome index for miniprot |
|
2 |
miRanda |
finds potential target sites for miRNAs in genomic sequences |
|
3 |
MiRDeep2 |
identification of novel and known miRNAs |
|
3 |
MiRDeep2 Mapper |
process and map reads to a reference genome |
|
3 |
MiRDeep2 Quantifier |
fast quantitation of reads mapping to known miRBase precursors |
|
2 |
Mismatch Profile |
calculates the distribution of mismatches across reads |
|
6 |
Missing Values Sample Filter |
- Remove samples with a high percentage of missing values |
|
2 |
MITObim |
mitochondrial baiting and iterative mapping |
|
1 |
MitoHiFi |
assembly mitogenomes from Pacbio HiFi reads |
Genome assembly
|
1 |
MitoID |
Infer the mitochondrial haplogroup from sequencing data |
|
1 |
MitoMatch |
Check for matching mitochondrial haplogroups of sequenced samples |
|
1 |
MITOS |
de-novo annotation of metazoan mitochondrial genomes |
|
2 |
MITOS2 |
de-novo annotation of metazoan mitochondrial genomes |
|
3 |
MiXCR Analyze |
immuno clonotyes from sequence data |
|
1 |
mixmodel |
ANOVA for repeated measures statistics |
|
1 |
MLST |
Scans genomes against PubMLST schemes |
|
4 |
MLST List |
Lists available schemes for the MLST tool |
|
4 |
MMPBSA/MMGBSA |
tool for estimating ligand binding affinities |
|
7 |
MOABS |
MOdel based Analysis of Bisulfite Sequencing data |
|
2 |
MOB-Recon |
Type contigs and extract plasmid sequences |
|
2 |
MOB-Typer |
Get the plasmid type and mobility given its sequence |
|
2 |
mockGenerator_from_test |
Generates mock repertoire from test library |
|
1 |
Model Prediction |
predicts on new data using a preffited model |
|
7 |
Model temporal trend |
with a simple linear regression |
|
1 |
Model temporal trend |
with a simple linear regression |
|
1 |
Model Validation |
includes cross_validate, cross_val_predict, learning_curve, and more |
|
11 |
ModiFastaId |
modified the id of fasta file.. |
|
1 |
Modify/convert GROMACS trajectories |
using trjconv and trjcat |
|
8 |
Module_Summary |
based on an taxonomic OTUreporter and modules |
|
1 |
moFF |
extracts MS1 intensities from spectrum files |
|
5 |
MOL to CML |
|
|
2 |
MOL to MOL2 |
|
|
2 |
MOL to SMILES |
|
|
2 |
MOL2 to CML |
|
|
2 |
MOL2 to InChI |
|
|
2 |
MOL2 to SDF |
|
|
2 |
MOL2 to SMILES |
|
|
2 |
mol2-to-mol |
converter |
|
2 |
Molecule recognition |
in PDF documents (OSRA) |
|
1 |
Molecule to fingerprint |
conversion to several different fingerprint formats |
|
5 |
Morpheus |
database search algorithm for high-resolution tandem mass spectra |
|
2 |
mothur.ref.taxonomy-to-mothur.seq.taxonomy |
converter |
|
2 |
mpileupfilterandstat |
Filter mpileup file entry |
|
1 |
mQC |
quality control of ribosome profiling mapping results |
|
2 |
MS-GF+ |
Identifies peptides in tandem mass spectra using the MS-GF+ search engine. |
|
5 |
MS-GF+ Percolator |
|
|
1 |
MSABOOT |
Output PHYLIP file with bootstrapped multiple sequence alignment data |
|
3 |
msbar |
Mutate sequence beyond all recognition |
|
5 |
MSConvert |
Convert non PSI standard mass spectral file into the PSI standard format mzML |
|
1 |
msconvert |
Convert and/or filter mass spectrometry files |
|
5 |
MSI classification |
spatial classification of mass spectrometry imaging data |
|
10 |
MSI colocalization |
mass spectrometry imaging colocalization |
|
1 |
MSI combine |
combine several mass spectrometry imaging datasets into one |
|
11 |
MSI data exporter |
exports imzML and Analyze7.5 to tabular files |
|
7 |
MSI filtering |
tool for filtering mass spectrometry imaging data |
|
8 |
MSI mz images |
mass spectrometry imaging m/z heatmaps |
|
8 |
MSI plot spectra |
mass spectrometry imaging mass spectra plots |
|
10 |
MSI preprocessing |
mass spectrometry imaging preprocessing |
|
11 |
MSI Qualitycontrol |
mass spectrometry imaging QC |
|
11 |
MSI segmentation |
mass spectrometry imaging spatial clustering |
|
8 |
MSI single ion segmentation |
mass spectrometry imaging spatial DGMM |
|
1 |
msms_extractor |
Extract MS/MS scans from the mzML file(s) based on PSM report |
|
1 |
MSnbase readMSData |
Imports mass-spectrometry data files |
|
3 |
msPurity.averageFragSpectra |
Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All) |
|
6 |
msPurity.createDatabase |
Create and SQLite database of an LC-MS(/MS) experiment |
|
6 |
msPurity.createMSP |
Create MSP files from msPurity processed data |
|
6 |
msPurity.dimsPredictPuritySingle |
Calculate the anticipated precursor ion purity from a DIMS dataset. |
|
6 |
msPurity.filterFragSpectra |
Filter fragmentations spectra associated with an XCMS feature |
|
6 |
msPurity.flagRemove |
Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds (e.g. RSD of intensity and retention time). |
|
6 |
msPurity.frag4feature |
Assign fragmentation spectra to XCMS features using msPurity |
|
6 |
msPurity.purityA |
Assess acquired precursor ion purity of MS/MS spectra |
|
6 |
msPurity.purityX |
Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset. |
|
6 |
msPurity.spectralMatching |
Perform spectral matching to MS/MS spectral libraries |
|
6 |
MSstats |
statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry |
|
5 |
MSstatsTMT |
protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling |
|
4 |
MT2MQ |
Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome |
|
3 |
Multi Compound Search |
an advanced molecular grep program using SMARTS |
|
2 |
Multi Compound Search |
an advanced molecular grep program using SMARTS |
|
1 |
Multi-Join |
(combine multiple files) |
|
10 |
multiBamSummary |
calculates average read coverages for a list of two or more BAM/CRAM files |
|
17 |
multiBigwigSummary |
calculates average scores for a list of two or more bigwig files |
|
17 |
MultiGPS |
analyzes collections of multi-condition ChIP-seq data |
|
1 |
Multilevel |
Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package |
|
1 |
Multipatt |
of a data frame |
|
1 |
Multiple BLASTN |
analyses agains a database |
|
1 |
MultipleAlignment |
of DNA or AA seqs |
|
1 |
Multiplicom Primer Trimmer |
|
|
1 |
MultiQC |
aggregate results from bioinformatics analyses into a single report |
Statistical calculation
Validation
Visualisation
|
18 |
Multivariate |
PCA, PLS and OPLS |
|
2 |
MUMmer |
: Compare genomes (Nucmer or Promer) |
|
1 |
Mummer |
Align two or more sequences |
Read mapping
Sequence alignment
|
5 |
MUMmer Clustering |
: order sequence matches in clusters |
|
1 |
MUMmer dotplot |
Combine mummer/nucmer/promer with mummerplot |
|
4 |
MUMmer MaxMatch |
: Maximal exact sequence matching |
|
1 |
MUMmer plot |
: Generate MUMmerplots from MUMmer match file |
|
1 |
MUMmer utilities |
: Show and filter on sequence delta file |
|
1 |
MUMmer2ACT |
: convert MUMmer comparison (coords) file to ACT (Artemis) |
|
1 |
Mummerplot |
Generate 2-D dotplot of aligned sequences |
Read mapping
Sequence alignment
|
5 |
MUSCLE |
multiple aligner |
Multiple sequence alignment
|
2 |
MuSiC Compare |
estimate and compare cell type proportions in multiple sets of bulk RNA-seq data |
|
2 |
MuSiC Deconvolution |
estimate cell type proportions in bulk RNA-seq data |
|
4 |
Mutate Codons |
with SNPs |
|
1 |
MuTect |
|
|
1 |
MyriMatch |
Identify peptides in tandem mass spectra. |
|
4 |
mz to sqlite |
Extract mzIdentML and associated proteomics datasets into a SQLite DB |
|
5 |
MzIdentML tools |
provides various functions to make workflows dealing with mzid files run smoothly |
|
1 |
mzIdentMLToJSON |
The tool to accelerate mzIdentML Viewer visualization plugin |
|
1 |
mzIdLib:combineSearchEngines |
Using mzIdentML-Lib to combine mzIdentML result files from different search engines |
|
1 |
mzIdLib:Converter |
Using mzIdentML-Lib to convert mzIdentML to CSV format. |
|
1 |
mzIdLib:FDR |
Using mzIdentML-Lib to calculate False Discovery Rate |
|
1 |
mzIdLib:ProteoGrouper |
Using mzIdentML-Lib to perform sequence-based protein inference |
|
1 |
mzIdLib:Threshold |
Using mzIdentML-Lib to remove identification under given threshold |
|
1 |
mzqLib:Converter |
Convert the mzQuantML file into more widely-used formats, e.g. CSV |
|
1 |
Naive Variant Caller (NVC) |
- tabulate variable sites from BAM datasets |
|
5 |
NanoComporeDB |
Process SampComp results database |
|
3 |
NanoFilt |
Filtering and trimming of long read sequencing data |
|
1 |
NanoPlot |
Plotting suite for Oxford Nanopore sequencing data and alignments |
|
6 |
Nanopolish eventalign |
- Align nanopore events to reference k-mers |
|
3 |
Nanopolish methylation |
- Classify nucleotides as methylated or not. |
|
3 |
Nanopolish polyA |
- Estimate the length of the poly-A tail on direct RNA reads. |
|
3 |
Nanopolish variants |
- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences |
|
3 |
NanopolishComp: EventalignCollapse |
by kmers rather than by event |
|
2 |
NanopolishComp: FreqMethCalculate |
calculates methylation frequency at genomic CpG sites |
|
1 |
NASTIseq |
Identify cis-NATs using ssRNA-seq |
|
1 |
Natural Product likeness calculator |
- calculates the similarity of the molecule to the structure space covered by known natural products |
|
3 |
NCBI Accession Download |
Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API |
|
3 |
NCBI BLAST+ blastdbcmd entry(s) |
Extract sequence(s) from BLAST database |
Data retrieval
Database search
|
18 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
19 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn for testing |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastn integrating BARLEX |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastp |
Search protein database with protein query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
19 |
NCBI BLAST+ blastp |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastp |
Search protein database with protein query sequence(s) |
|
1 |
NCBI BLAST+ blastp |
Search protein database with protein query sequence(s) |
|
1 |
NCBI BLAST+ blastp |
Search protein database with protein query sequence(s) |
|
1 |
NCBI BLAST+ blastp |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastp |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastp |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastp for testing |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastx |
Search protein database with translated nucleotide query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
18 |
NCBI BLAST+ blastx |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastx |
Search protein database with translated nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastx |
Search protein database with translated nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastx |
Search protein database with translated nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastx |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastx |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ blastx |
Search nucleotide database with nucleotide query sequence(s) |
|
1 |
NCBI BLAST+ convert2blastmask |
Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb |
Conversion
|
15 |
NCBI BLAST+ database info |
Show BLAST database information from blastdbcmd |
Data retrieval
|
18 |
NCBI BLAST+ dustmasker |
masks low complexity regions |
Sequence complexity calculation
|
16 |
NCBI BLAST+ makeblastdb |
Make BLAST database |
Genome indexing
|
18 |
NCBI BLAST+ makeprofiledb |
Make profile database |
Genome indexing
|
14 |
NCBI BLAST+ rpsblast |
Search protein domain database (PSSMs) with protein query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
17 |
NCBI BLAST+ rpstblastn |
Search protein domain database (PSSMs) with translated nucleotide query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
17 |
NCBI BLAST+ segmasker |
low-complexity regions in protein sequences |
Sequence complexity calculation
|
15 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
19 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastn |
Search translated nucleotide database with protein query sequence(s) |
|
1 |
NCBI BLAST+ tblastx |
Search translated nucleotide database with translated nucleotide query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
19 |
NCBI Datasets Genomes |
download genome sequence, annotation and metadata |
|
12 |
NCBI get species taxids |
|
|
2 |
NCBIRef16SrRNA |
retrieve corresponding 16S rRNA gene from NCBIrefgenome. |
|
1 |
Nearest Neighbors Classification |
|
|
11 |
needle |
Needleman-Wunsch global alignment |
|
5 |
Neoepitope Finder: |
Predict neoepitopes for SNVs called using CCCP |
|
1 |
neostore.zip-to-neostore |
converter |
|
1 |
Netcdf Metadata Info |
summarize content of a nc file |
|
1 |
Netcdf Reader |
extracts variable values with custom conditions on dimensions |
|
1 |
NetCDF xarray Coordinate Info |
Get values for each coordinate of a Netcdf file |
|
4 |
NetCDF xarray map plotting |
Visualize netCDF variables on a geographical map |
|
3 |
NetCDF xarray Metadata Info |
summarize content of a Netcdf file |
|
5 |
NetCDF xarray operations |
manipulate xarray from netCDF and save back to netCDF |
|
3 |
NetCDF xarray Selection |
extracts variable values with custom conditions on dimensions |
|
5 |
NetCoverage |
calculate the coverage of modules in different samples |
|
1 |
NetworkComparisons |
calculate the distance between networks |
|
1 |
newcpgreport |
Report CpG rich areas |
|
5 |
newcpgseek |
Reports CpG rich region |
|
5 |
Newick Display |
visualize a phylogenetic tree |
Phylogenetic tree visualisation
|
2 |
newseq |
Type in a short new sequence |
|
5 |
NextAlign |
Viral genome sequence alignment |
|
15 |
Nextclade |
Viral genome clade assignment, mutation calling, and sequence quality checks |
|
18 |
NG-CHM Generator |
Create Clustered Heat Maps |
|
3 |
NG-Tax 2 |
|
|
1 |
NGSfilter |
Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers |
|
3 |
NGTax Uploader |
|
|
1 |
nhmmer |
search a DNA model or alignment against a DNA database (BLASTN-like) |
|
8 |
nhmmscan |
search DNA sequence(s) against a DNA profile database |
|
8 |
Nmds |
generate non-metric multidimensional scaling data |
|
6 |
NMMD |
based on a dataframe |
|
1 |
NMMD |
based on a dist matrix |
|
1 |
NMR spectra alignment |
based on the Cluster-based Peak Alignment (CluPA) algorithm |
|
2 |
NMR_Annotation |
Annotation of complex mixture NMR spectra and metabolite proportion estimation |
|
1 |
NMR_Bucketing |
Bucketing and integration of NMR Bruker raw data |
|
4 |
NMR_Preprocessing |
Preprocessing of 1D NMR spectra |
|
4 |
NMR_Read |
Read Bruker NMR raw files |
|
3 |
Nonpareil |
to estimate average coverage and generate Nonpareil curves |
|
2 |
noreturn |
Removes carriage return from ASCII files |
|
5 |
Normalization |
Normalization of (preprocessed) spectra |
|
4 |
Normalize |
combined meta'omic sequencing data |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Normalize |
combined meta'omic sequencing data |
|
3 |
Normalize |
with scanpy |
|
7 |
Normalize a dataset by |
row or column sum to obtain proportion or percentage |
|
1 |
Normalize by Copy Number |
|
|
1 |
Normalize.shared |
Normalize the number of sequences per group to a specified level |
|
5 |
NormalizeFasta |
normalize fasta datasets |
|
14 |
notseq |
Exclude a set of sequences and write out the remaining ones |
|
5 |
NOVOplasty |
de novo assembler for short circular genomes |
|
3 |
NSAF Scoring Table |
|
|
1 |
NSPDK_candidateClusters |
|
|
4 |
NSPDK_sparseVect |
|
|
4 |
nthseq |
Writes one sequence from a multiple set of sequences |
|
5 |
NucBed |
profile the nucleotide content of intervals in a FASTA file |
|
21 |
Nucleolar localization sequence Detector (NoD) |
Find nucleolar localization signals (NoLSs) in protein sequences |
|
3 |
Nucleosome Predictions |
|
|
1 |
Nucleotide Diversity |
: π and θ |
|
2 |
Nucleotide subsequence search |
providing regions in BED format |
|
2 |
Nucmer |
Align two or more sequences |
Read mapping
Sequence alignment
|
5 |
Numeric Clustering |
|
|
12 |
NxN clustering |
of molecular fingerprints |
|
5 |
obiannotate |
Adds/Edits sequence record annotations |
|
3 |
obiclean |
tags a set of sequences for PCR/sequencing errors identification |
|
3 |
obiconvert |
converts sequence files to different output formats |
|
3 |
obigrep |
Filters sequence file |
|
3 |
obisort |
sorts sequence records according to the value of a given attribute |
|
3 |
obistat |
computes basic statistics for attribute values |
|
3 |
obitab |
converts sequence file to a tabular file |
|
3 |
obiuniq |
|
|
3 |
Obtain |
a list of entries identifier and associated defination from KEGG(www.kegg.jp) |
|
1 |
occ_to_fasta |
regroup peptides to fasta |
|
1 |
ococo |
consensus caller on SAM/BAM |
|
1 |
octanol |
Displays protein hydropathy |
|
5 |
oddcomp |
Find protein sequence regions with a biased composition |
|
5 |
odgi build |
construct a dynamic succinct variation graph |
|
2 |
odgi viz |
variation graph visualizations |
|
2 |
Off Target Coverage Report |
|
|
1 |
OGR Informations |
lists information about an OGR supported data source |
|
2 |
OGR2ogr |
converts simple features data between file formats |
|
2 |
One Way Multicomp |
using TukeyHSD tests |
|
1 |
One Way Multicomp |
using glm model for binary data(negative binomial test.) |
|
1 |
One_Way_Multicomp3 |
using TukeyHSD or negative binomical tests |
|
1 |
OneWayOptimizationPCA |
analyses and plot |
|
1 |
Online data |
fetching ... |
|
2 |
ont_fast5_api: Compress |
multi read file(s) |
|
2 |
ont_fast5_api: Multi to single |
read file(s) |
|
2 |
ont_fast5_api: Single to multi |
read file(s) |
|
2 |
ont_fast5_api: Subset |
of multi read file(s) |
|
3 |
Open 3D Align |
with RDKit |
|
2 |
Open Molecule Generator |
- exhaustive generation of chemical structures |
|
3 |
OpenDUck chunk |
for dynamic undocking |
|
1 |
OpenPepXL |
Tool for protein-protein cross-linking identification using labeled linkers. |
|
4 |
Operate on pixels |
with a mathematical expression |
|
2 |
OPLS-DA_Contrasts |
OPLS-DA Contrasts of Univariate Results |
|
5 |
OptiType |
HLA genotyping predictions from NGS data |
|
1 |
ORFfinder |
(open reading frame) finder using fasta sequences |
|
1 |
ORFipy |
a versatile ORF finder |
|
2 |
OrthoFinder |
finds orthogroups in a set of proteomes |
|
7 |
Otu.association |
Calculate the correlation coefficient for the otus |
|
5 |
Otu.hierarchy |
Relate OTUs at different distances |
|
5 |
Overall FST |
: Estimate the relative fixation index between two populations |
|
4 |
Overlapped_seqs |
between bidirectional sequences |
|
1 |
Overlay |
moving and fixed image |
|
1 |
Overlay Images |
for visualization |
|
2 |
Overlay Segmentation Mask |
Overlay Segmentation Mask |
|
1 |
OverlayOutlines |
places outlines of objects over a desired image. |
|
2 |
Owler |
fast, trimmed overlap pipeline without aligning |
|
1 |
PACKMOL |
- initial configurations for molecular dynamics simulations by packing optimization |
|
2 |
PaDEL descriptor |
calculator |
|
1 |
Paired barplot |
of two data frame or one data frame |
|
1 |
Paired Correlation |
between two dataframe |
|
1 |
Paired FastQ QC-Trimmer |
|
|
1 |
Paired Read Mate Fixer |
for paired data |
|
3 |
Paired-end histogram |
of insert size frequency |
|
1 |
Pairs sequenced |
: Offspring estimated heterozygosity of sequenced pairs |
|
2 |
Pairwise intersection |
and heatmap for genomic intervals |
|
4 |
Pairwise Mantel |
tests among distance matrix or dataframe. |
|
1 |
Pairwise.seqs |
calculate uncorrected pairwise distances between sequences |
|
5 |
palindrome |
Looks for inverted repeats in a nucleotide sequence |
|
5 |
Panel Coverage Report |
|
|
1 |
Pangolin |
Phylogenetic Assignment of Outbreak Lineages |
|
22 |
Para2sents |
split paragraph into sentences(text) |
|
1 |
Parallel Coordinates Plot |
of tabular data |
|
3 |
PARalyzer |
A method to map interaction sites between RNA-binding proteins and their targets |
|
1 |
ParmChk2 |
- Amber's parameter checker |
|
8 |
parquet-to-csv |
converter |
|
1 |
Parse |
Blast reporter |
|
1 |
Parse 16S BlastN resport. |
|
|
1 |
Parse Article |
Parse articles using python |
|
1 |
Parse blast XML output |
|
|
2 |
Parse mitochondrial blast |
overlap-conscious coverage calculation between scaffold-accession number pairs from blast output |
|
2 |
parse mykrobe predict |
for Shigella sonnei and tabulate results into a single tab-delimited file |
|
1 |
Parse.list |
Generate a List file for each group |
|
5 |
ParseBlastForUniqueMatch |
Filter mpileup with blast results |
|
1 |
Parsimony |
Describes whether two or more communities have the same structure |
|
5 |
Partition genes into expression clusters |
after differential expression analysis using a Trinity assembly |
|
12 |
PASS |
significant transcription factor binding sites from ChIP data |
|
1 |
Paste |
two files side by side |
|
1 |
pasteseq |
Insert one sequence into another |
|
5 |
Pathview |
for pathway based data integration and visualization |
|
3 |
Pathway Image |
: Draw a KEGG pathway, highlighting specified gene modules |
|
3 |
Pathway/GeneSets |
expression based RPKM of genesets. |
|
1 |
Pathway/Genesets |
enrichment analysis using Gesa. |
|
1 |
Pathway/Module2genes |
gene list of pathway. |
|
1 |
patmatdb |
Search a protein sequence with a motif |
|
5 |
Pca |
Principal Coordinate Analysis for a shared file |
|
6 |
PCA |
analyses and plot |
|
1 |
PCA |
: Principal Component Analysis of genotype data |
|
3 |
PCA |
- principal component analysis using Bio3D |
|
2 |
PCA plot w ggplot2 |
|
|
7 |
PCA visualization |
- generate trajectories of principal components of atomic motion |
|
2 |
Pcoa |
Principal Coordinate Analysis for a distance matrix |
|
5 |
PCoA |
based on a dist matrix |
|
1 |
Pcr.seqs |
Trim sequences |
|
6 |
pdb-to-gro |
converter |
|
1 |
PDF2TEXT |
Transformation PDF into Text. |
|
1 |
pe-sync: Paired-end synchronization check |
The Paired-end synchronization check program determines if the reads in paired-end fastq files are in the proper order (synchronized). |
|
2 |
Pear |
Paired-End read merger |
|
5 |
pepcoil |
Predicts coiled coil regions |
|
5 |
pepGenerator2 |
Generate mock peptides |
|
1 |
pepinfo |
Plots simple amino acid properties in parallel |
|
5 |
PepMatch |
align PSTs on sequence and cluster hits |
|
1 |
pepnet |
Displays proteins as a helical net |
|
5 |
PepNovoTag |
generate short Peptide Sequence Tags (PSTs) from MS/MS spectra file |
|
1 |
PepPointer |
classify genomic location of peptides |
|
2 |
pepProfileRatio |
ratio profile 1/profile 2 |
|
1 |
PepQuery |
Peptide-centric search engine for novel peptide identification and validation. |
|
4 |
pepSimili |
pepSimili workflow |
|
1 |
pepstats |
Protein statistics |
|
5 |
Pept_to_fasta |
convert peptides file to fasta |
|
1 |
PepteamMap |
create mapping |
|
1 |
PepteamProfile |
mapping to profile |
|
1 |
PepteamScoring |
PepteamScoring |
|
1 |
Peptide Genomic Coordinate |
Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB |
|
2 |
Peptide MW and hydrophobicity |
Calculate the molecular weight and hydrophobicity for peptides within a fasta file |
|
1 |
Peptide Shaker |
Perform protein identification using various search engines based on results from SearchGUI |
|
19 |
Peptide spectrum matching |
Using SearchGUI to perform MS/MS search via X!Tandem, OMSSA and MS-GF+ |
|
1 |
peptide2protein_mapping |
create peptide to protein mapping |
|
1 |
peptides occurences in repertoire |
measures peptides occurrences |
|
1 |
PepTree |
.fastIdx to .pepTree.x |
|
1 |
pepwheel |
Shows protein sequences as helices |
|
5 |
pepwindow |
Displays protein hydropathy |
|
5 |
pepwindowall |
Displays protein hydropathy of a set of sequences |
|
5 |
Per-SNP FSTs |
: Compute a fixation index score for each SNP |
|
3 |
Perform Best-subsets Regression |
|
|
2 |
Perform LDA |
Linear Discriminant Analysis |
|
2 |
Perform Linear Regression |
|
|
1 |
Perform Logistic Regression with vif |
|
|
1 |
Perform metadata association |
on HUMAnN generated table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Permutate image |
along an axis |
|
2 |
Permutation test |
based on a hybridized distance matrix or similarity matrix. |
|
1 |
Permutation test |
to analyze significant difference between community composition based on a pairwise distance matrix |
|
1 |
PGAP |
genomes annotation using NCBI PGAP pipeline. |
|
1 |
pgma_graphclust |
|
|
3 |
PharmaADMEntor |
Flag variants found in the PharmaADME database |
|
1 |
Pharmacophore |
generation (Align-it) |
|
3 |
Pharmacophore alignment |
and optimization (Align-it) |
|
3 |
pharmCAT |
Pharmacogenomics Clinical Annotation Tool |
|
2 |
phmmer |
search a protein sequence against a protein database (BLASTP-like) |
|
8 |
Phylip |
: prepare data for phylogenetic analysis |
|
2 |
Phylo.diversity |
Alpha Diversity calculates unique branch length |
|
5 |
Phylogenetic Tree |
: Show genetic relationships among individuals |
|
3 |
phyloP |
interspecies conservation scores |
|
1 |
Phylorelatives |
Relatedness of minor alelle sequences in NJ tree |
|
1 |
Phyloseq: plot alpha diverstiy measure |
|
|
1 |
Phyloseq: plot ordination |
|
|
1 |
Phylotype |
Assign sequences to OTUs based on taxonomy |
|
5 |
PhyML |
Phylogeny software based on the maximum-likelihood method. |
Phylogenetic analysis
Phylogenetic inference (from molecular sequences)
|
4 |
Phyogenetic reconstruction with RAxML |
- Maximum Likelihood based inference of large phylogenetic trees |
|
6 |
Picard Collect Sequencing Artifact Metrics |
Collect metrics to quantify single-base sequencing artifacts |
|
6 |
Pick |
diverse compounds from a library with Butina clustering |
|
2 |
Pick Fasta sequences |
with header satisfying a string query |
Filtering
|
2 |
Pick Primers |
: Find suitable PCR primers for SNPs |
|
2 |
Pieplot |
of dataframe. |
|
1 |
Pileup to VCF |
Converts a pileup to VCF with filtering |
|
2 |
Pileup-to-Interval |
condenses pileup format into ranges of bases |
|
4 |
PileupVariant |
Keep only mpileup line with variant |
|
1 |
pilon |
An automated genome assembly improvement and variant detection tool |
|
2 |
Pipeline Builder |
an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers |
|
11 |
PIPmiR PIPELINE |
a method to identify novel plant miRNA |
|
1 |
Piranha |
peak-caller for CLIP- and RIP-Seq data |
|
1 |
PIT:DIAMOND stratify |
- Stratified search using sequential databases to reduce search times |
|
1 |
PIT:Extract hits |
Extract peptide information from various file formats for PIT analysis |
|
1 |
PIT:FASTA ORFs 2 |
- Find the longest ORFs in non-mapped transcripts |
|
1 |
PIT:Get sequences for identified proteins |
Get identified protein sequences |
|
1 |
PIT:Integrate |
The tool links sam file to the peptide identification file with the defined regular expression |
|
1 |
PIT:MSGF integrate 2 |
- Integrate MSGF peptides with PacBio ORFs |
|
1 |
PIT:MSGF integrate representative |
- Integrate MSGF peptides with PacBio representative ORFs |
|
1 |
PIT:MSGF peptides remove |
- Remove known peptides using peptides lists from MSGF |
|
1 |
PIT:ORFall |
The ORF prediction tool |
|
1 |
PIT:Protein homology |
Use BLAST to find protein homology and source species |
|
1 |
PIT:Protein Summary |
Provides a tabular summary of the characteristics of protein sequence files |
|
1 |
PIT:PSM PostProcessing |
Using mzIdentML-Lib to do some post processing including FDR calculation etc. |
|
1 |
pizzly |
- fast fusion detection using kallisto |
|
2 |
PlasFlow |
Prediction of plasmid sequences in metagenomic contigs |
|
1 |
plasmidSPAdes |
extract and assembly plasmids from WGS data |
|
6 |
plink |
|
|
6 |
Plot |
with scanpy |
|
8 |
Plot abundance |
with trend line |
|
1 |
Plot abundance |
with trend line |
|
1 |
Plot actual vs predicted curves and residual plots |
of tabular data |
|
1 |
Plot confusion matrix, precision, recall and ROC and AUC curves |
of tabular data |
|
2 |
Plot Distribution |
Plot Distribution |
|
1 |
Plot performance |
per cell in nanopore reads |
|
2 |
Plot signals |
for nanopore reads |
|
2 |
Plot_Distmatrix |
plot a distance matrix. |
|
1 |
Plot_image |
plot images of a dataframe |
|
1 |
Plot_Rare_lines |
of a rarefaction table |
|
1 |
plotcon |
Plot quality of conservation of a sequence alignment |
|
5 |
plotCorrelation |
Create a heatmap or scatterplot of correlation scores between different samples |
|
16 |
plotCoverage |
assesses the sequencing depth of BAM/CRAM files |
|
16 |
plotDEXSeq |
Visualization of the per gene DEXSeq results |
|
5 |
plotEnrichment |
plots read/fragment coverage over sets of regions |
|
12 |
plotFingerprint |
plots profiles of BAM files; useful for assesing ChIP signal strength |
|
17 |
plotHeatmap |
creates a heatmap for score distributions across genomic regions |
|
17 |
plotorf |
Plot potential open reading frames |
|
5 |
plotPCA |
Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output |
|
16 |
plotProfile |
creates a profile plot for score distributions across genomic regions |
|
16 |
Plots |
based on data frames. |
|
1 |
Plotting tool |
for multiple series and graph types |
|
5 |
PLSDA |
analyses and plot |
|
1 |
Points to Label |
Points to Label Image |
|
1 |
Poisson two-sample test |
|
|
1 |
polydot |
Displays all-against-all dotplots of a set of sequences |
|
5 |
Population Complexity |
: Evaluate possible numbers of ancestral populations |
|
2 |
Porechop |
adapter trimmer for Oxford Nanopore reads |
|
3 |
Pos2LDBlock |
Map a position in the genome to the LD block. |
|
1 |
Pre.cluster |
Remove sequences due to pyrosequencing errors |
|
5 |
Predict Metagenome |
|
|
1 |
Predict variant effects |
with VEP |
|
3 |
preg |
Regular expression search of a protein sequence |
|
6 |
PREGO |
A software tool that predicts high responding peptides for SRM experiments |
|
1 |
Prepare Input |
: Filter and convert to the format needed for these tools |
|
4 |
Prepare ligand |
for docking with Autodock Vina |
|
1 |
Prepare ligands for docking |
Tool to prepare ligands for docking with tools like Autodock Vina |
|
4 |
Prepare receptor |
Tool to prepare receptor for docking with Autodock Vina |
|
2 |
PrepareFastqLight |
Fastq preparation |
|
1 |
Preprocess |
raw feature vectors into standardized datasets |
|
12 |
Preprocess files for SARTools |
generate design/target file and archive for SARTools inputs |
|
4 |
Preprocess population data |
for evolution trend analyzes |
|
2 |
Preprocessing |
|
|
4 |
Presence-absence and abundance |
Community abundance map, presence barplot and rarefaction curves |
|
1 |
pRESTO AlignSets |
Multiple-align sequences with the same barcodes. |
|
3 |
pRESTO AssemblePairs |
Assembles paired-end reads into a single sequence. |
|
3 |
pRESTO BuildConsensus |
Builds a consensus sequence for each set of input sequences |
|
3 |
pRESTO CollapseSeq |
Remove/collapse duplicate sequences |
|
3 |
pRESTO FilterSeq |
Filters and/or masks reads based on length, quality, missing bases and repeats. |
|
3 |
pRESTO MaskPrimers |
Removes primers and annotates sequences with primer and barcode identifiers. |
|
3 |
pRESTO PairSeq |
Sorts and matches sequence records with matching coordinates across files |
|
3 |
pRESTO ParseHeaders |
Manage annotations in FASTQ headers. |
|
3 |
pRESTO ParseLog |
Create tabular report from pRESTO log file |
|
3 |
pRESTO Partition |
Partition a file in two |
|
3 |
pRESTOr AbSeq3 Report |
Create HTML QC report from pRESTO outputs |
|
4 |
Pretext Snapshot |
|
|
2 |
PretextMap |
converts SAM or BAM files into genome contact maps |
|
7 |
prettyplot |
Displays aligned sequences, with colouring and boxing |
|
5 |
prettyseq |
Output sequence with translated ranges |
|
5 |
Primer Designer: |
Design primers for AmpliSeq AccessArray or Sanger resequencing of given SNVs |
|
1 |
Primer Developer |
Primer developer for Sanger sequencing. |
|
1 |
Primer.design |
identify sequence fragments that are specific to particular OTUs |
|
5 |
primersearch |
Searches DNA sequences for matches with primer pairs |
|
5 |
Principal Component Analysis |
|
|
1 |
Principal component analysis |
with scikit-learn |
|
3 |
PRINSEQ |
to process quality of sequences |
|
5 |
Print Reads |
on BAM files |
|
3 |
Print Reads |
from BAM files |
|
1 |
Prioritizer |
Combine various Dintegrator modules to perform integrative gene prioritization. |
|
1 |
Process Scans (and SIM-Stitch) |
- Read, filter and average MS scans |
|
2 |
ProcessSomatic |
Extract HC calls from Somatic Caller |
|
1 |
PRODIGAL |
predict prokaryotic genes |
|
1 |
proFIA |
Preprocessing of FIA-HRMS data |
|
2 |
Profile Annotations |
for a set of genomic intervals |
|
1 |
progressiveMauve |
constructs multiple genome alignments |
|
3 |
ProHits DotPlot Generator |
|
|
1 |
Projective Transformation |
Projective Transformation |
|
4 |
Projective Transformation |
of input points |
|
5 |
Prokka |
Prokaryotic genome annotation |
Coding region prediction
Gene prediction
Genome annotation
|
11 |
Promoter 2.0 |
Find eukaryotic PolII promoters in DNA sequences |
|
5 |
proportional venn |
from 2-3 sets |
|
1 |
Protease prediction |
based on cleavage sites |
|
3 |
Protein Database Downloader |
|
|
6 |
Proteinortho |
detects orthologous proteins/genes within different species |
|
5 |
Proteinortho grab proteins |
finds genes/proteins in a given fasta file |
|
5 |
Proteinortho summary |
summaries the orthology-pairs/RBH files |
|
5 |
Proteomiqon JoinQuantPepIonsWithProteins |
combines the results from ProteinInference and PSMBasedQuantification. |
|
1 |
Proteomiqon LabeledProteinQuantification |
estimates protein abundances using quantified peptide ions. |
|
1 |
Proteomiqon LabelFreeProteinQuantification |
estimates protein abundances using quantified peptide ions. |
|
1 |
ProteomIQon MzMLToMzLite |
converts mzML files to mzLite files. |
|
2 |
ProteomIQon PeptideDB |
creates a peptide database in the SQLite format. |
|
1 |
ProteomIQon PeptideSpectrumMatching |
iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches. |
|
1 |
ProteomIQon ProteinInference |
uses identified peptides to infere proteins explaining their presence in the sample. |
|
1 |
Proteomiqon PSMBasedQuantification |
allows label-free quantification as well as quantification of full metabolic labeled samples. |
|
2 |
ProteomIQon PSMStatistics |
utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. |
|
3 |
PSM-Fragment Validator |
Validate PSMs against Ion Fragmentation |
|
2 |
psortb |
Determines sub-cellular localisation of bacterial/archaeal protein sequences |
|
5 |
PubChem Assay Downloader |
as canonical SMILES |
|
3 |
PubChem Download |
as canonical SMILES |
|
3 |
Purge overlaps |
and haplotigs in an assembly based on read depth (purge_dups) |
|
6 |
Pycoqc |
|
|
1 |
PyCoreGenome |
calculate pearson and spearman correlation for a dataframe. |
|
1 |
PyCorrelation |
calculate pearson and spearman correlation for a dataframe. |
|
1 |
PyDataManager |
modify dataframe using python3 packages. 利用Pandas包操作数据框。 |
|
1 |
PyDatatransform |
transform dataset using python3 packages. |
|
1 |
pyGenomeTracks |
plot genomic data tracks |
|
12 |
PyProphet export |
Export tabular files, optional swath2stats export |
|
2 |
PyProphet merge |
Merge multiple osw files |
|
1 |
PyProphet peptide |
Peptide error-rate estimation |
|
1 |
PyProphet protein |
Protein error-rate estimation |
|
1 |
PyProphet score |
Error-rate estimation for MS1, MS2 and transition-level data |
|
3 |
PyProphet subsample |
Subsample OpenSWATH file |
|
1 |
pyteomics |
convert mztab to tabular |
Conversion
|
1 |
Qiime2RDP |
Qiime classifier to RDP classifier |
|
1 |
QualiMap BamQC |
|
|
5 |
QualiMap Counts QC |
|
|
2 |
QualiMap Multi-Sample BamQC |
|
|
2 |
QualiMap RNA-Seq QC |
|
|
3 |
Quality format converter |
(ASCII-Numeric) |
|
3 |
Quality Metrics |
Metrics and graphics to check the quality of the data |
|
2 |
QualityScoreDistribution |
chart quality score distribution |
|
14 |
QuanTP |
Correlation between protein and transcript abundances |
|
2 |
QuantWiz-IQ |
Isobaric Quantitation using QuantWiz-IQ |
|
1 |
Quast |
Genome assembly Quality |
|
14 |
Query Article DB |
for sentences with keywords. |
|
1 |
Query CRAPome |
|
|
1 |
Query Tabular |
using sqlite sql |
|
8 |
Racon |
Consensus module for raw de novo DNA assembly of long uncorrected reads |
|
8 |
Radfit |
analysis of a taxonomic otu reporter. |
|
1 |
Ramachandran Analysis |
- Ramachandran plot for proteins |
|
2 |
Ramachandran Plots |
- calculate and plot the distribution of two dihedrals in a trajectory |
|
4 |
RandomForest |
to identify key tax discrimnative among treatments. |
|
1 |
RandomSamplingSeqs |
retrieve randomly from the fasta files |
|
1 |
Rank Pathways |
: Assess the impact of a gene set on KEGG pathways |
|
4 |
Rank Terms |
: Assess the enrichment/depletion of a gene set for GO terms |
|
3 |
RankedStack |
plot the number of responding genes according to responding level and taxa. |
|
1 |
RAPT |
assemble and annotation of genomes. |
|
1 |
Rarefaction |
analysis of a taxonomic OTU reporters |
|
1 |
Rarefaction.shared |
Generate inter-sample rarefaction curves for OTUs |
|
5 |
Rarefaction.single |
Generate intra-sample rarefaction curves for OTUs |
|
6 |
Raven |
De novo assembly of Oxford Nanopore Technologies data |
|
5 |
Raw Tools |
Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files. |
|
1 |
RAxML |
: construct a maximum-likelihood phylogenetic tree |
|
2 |
RCAS |
- RNA Centric Annotation System |
|
2 |
RDA |
analyses and plot |
|
1 |
RDA/CCA/NMMD |
analyses and plot |
|
1 |
Rdata binary file reader |
|
|
1 |
Rdata parser |
|
|
1 |
RDConf: Low-energy ligand conformer search |
using RDKit |
|
1 |
RDF Analysis |
- Radial Distribution Function between two atoms |
|
4 |
RDF Format |
Converter (Rapper) |
|
1 |
rDock cavity definition |
- generate the active site definition needed for rDock docking |
|
2 |
rDock docking |
using the sdsort provided with rDock |
|
3 |
rDock docking |
- perform protein-ligand docking with rDock |
|
6 |
RDP classifier(2.01) |
of sequences data |
|
1 |
RDP MultiClassifier |
Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy |
|
1 |
Re-align with SRMA |
|
|
1 |
Reaction maker |
using RDKit |
|
2 |
Reaction SMARTS filter |
using RDKit |
|
2 |
Reactivity Calculation |
calculates structural reactivity on each nucleotide based on RT stop counts from the Get RT Stop Counts module |
|
1 |
ReactomeAnnotator |
Accesses information from Reactome |
|
1 |
Read Distribution |
calculates how mapped reads were distributed over genome feature |
|
12 |
Read Duplication |
determines reads duplication rate with sequence-based and mapping-based strategies |
|
10 |
Read GC |
determines GC% and read count |
|
10 |
Read It and Keep |
|
|
2 |
Read length statistics |
from a set of FAST5 files |
|
2 |
Read name modifier |
--change space to underscore in the read name column |
|
1 |
Read NVC |
to check the nucleotide composition bias |
|
10 |
Read Quality |
determines Phred quality score |
|
10 |
Realign reads |
with LoFreq viterbi |
|
5 |
Realigner Target Creator |
for use in local realignment |
|
3 |
Realigner Target Creator |
for use in local realignment |
|
1 |
Rebase GFF3 features |
against parent features |
|
2 |
Reduce |
a joined HUMAnN table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Reduce |
a HUMAnN2 generated table |
|
4 |
Reduce Reads |
in BAM files |
|
3 |
Regex Find And Replace |
|
|
5 |
Regex Replace |
Regular Expression replacement using the Python re module |
|
1 |
Regroup |
HUMAnN table features |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Regroup |
a HUMAnN2 generated table by features |
|
4 |
Reheader |
copy SAM/BAM header between datasets |
|
4 |
RelateObjects |
assign relationships parent-children between objects |
|
2 |
Relative/Absolute abundance |
of a data frame |
|
1 |
Remarkable Intervals |
: Find high-scoring runs of SNPs |
|
3 |
Remove beginning |
of a file |
|
1 |
Remove columns |
by heading |
|
2 |
Remove confounders |
with scanpy |
|
7 |
Remove counterions and fragments |
|
|
2 |
Remove counterions and fragments |
from a library of compounds |
|
7 |
Remove duplicated molecules |
|
|
1 |
Remove duplicated molecules |
from a library of compounds |
|
5 |
Remove Fasta sequences |
from a file |
|
1 |
Remove OTUs |
of a complex inoculant |
|
1 |
Remove protonation state |
of every atom |
|
1 |
Remove protonation state |
of every atom |
|
6 |
Remove Rare OTU |
From an OTU reporter |
|
1 |
Remove sequencing artifacts |
|
|
5 |
Remove small molecules |
|
|
1 |
Remove small molecules |
from a library of compounds |
|
5 |
Remove Unwanted Variation |
from RNA-seq data |
|
4 |
Remove.dists |
Removes distances from a phylip or column file |
|
6 |
Remove.groups |
Remove groups from groups,fasta,names,list,taxonomy |
|
5 |
Remove.lineage |
Picks by taxon |
|
5 |
Remove.otulabels |
Removes OTU labels |
|
6 |
Remove.otus |
Removes OTUs from various file formats |
|
5 |
Remove.rare |
Remove rare OTUs |
|
5 |
Remove.seqs |
Remove sequences by name |
|
6 |
Remove_columns |
Remove one or several columns by number or label |
|
1 |
remove_tab_dupes |
Finds duplicates in tab format files |
|
1 |
remuRNA |
Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation |
|
1 |
Rename |
features of a HUMAnN2 generated table |
|
4 |
Rename Fasta |
by sequence description |
|
1 |
Rename features |
of a HUMAnN generated table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Rename samples |
in a data frame |
|
1 |
Rename seq |
of a fasta in batch mode |
|
1 |
Rename seq2 |
Multiple Sequences |
|
1 |
Rename sequences |
|
|
5 |
Rename.seqs |
Rename sequences by concatenating the group name |
|
2 |
RenameDistMatrix |
rename the distance matrix according to sampcood2sampname. |
|
1 |
RenameTarfile |
rename files in a tar folders. |
|
1 |
Renormalize |
a HUMAnN generated table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
3 |
Renormalize |
a HUMAnN2 generated table |
|
5 |
Reorder individuals |
: exchange rows in the above picture |
|
2 |
ReorderSam |
reorder reads to match ordering in reference sequences |
|
17 |
RepeatMasker |
screen DNA sequences for interspersed repeats and low complexity regions |
Repeat sequence analysis
|
8 |
RepeatModeler |
Model repetitive DNA |
|
2 |
Replace |
parts of text |
|
12 |
Replace ambiguous codons |
in a multiple alignment using HyPhy |
|
4 |
Replace column |
by values which are defined in a convert file |
|
2 |
Replace Text |
in entire line |
|
11 |
Replace Text |
in a specific column |
|
11 |
Replace with original headers |
Replace the header generated by Fasta Header Manipulation serial option with its original header |
|
1 |
ReplaceSamHeader |
replace header in a SAM/BAM dataset |
|
17 |
Replicate Filter |
- Remove peaks that fail to appear in at least x-out-of-n (technical) replicates |
|
2 |
RepMatch |
Match paired peaks from two or more replicates |
|
3 |
Representative seqs |
of a set of fasta sequences |
|
1 |
Resampling |
- determine per-gene p-values |
|
5 |
Resize coordinate window |
of GFF data |
|
3 |
RespondingBox/Barplot |
identify association between responses and envparaments |
|
1 |
RespondingJaccard |
calculate responding patterns |
|
1 |
RespondingPairedBar |
Based on statistic tables |
|
1 |
Restore Attributes |
: Fill in missing properties for a gd_snp or gd_genotype dataset |
|
3 |
resync |
Resynchronize pairs of paired-end fastq files |
|
2 |
Retrieve |
given database entries from KEGG(www.kegg.jp) |
|
1 |
Retrieve Data |
from Apollo into Galaxy |
|
8 |
Retrieve FASTA from NCBI |
|
Data retrieval
|
2 |
Retrieve JBrowse |
for an organism, from Apollo |
|
8 |
Retrieve Key Sentences |
from a paper or web page.(So far, Only english) |
|
1 |
Retrieve Sequences |
from a blast databases.. |
|
1 |
Retrieve16S/18S |
rRNA gene from metagenomic library. |
|
1 |
Retrieve_Seqs |
based on sample names. |
|
1 |
RetrieveMap |
from data from the mapping . |
|
1 |
RetrieveSeq |
with high similarity to the provided reference from a metagenomic library . |
|
1 |
Retrive |
all genes of a KEGG organisms(www.kegg.jp) |
|
1 |
RetriveDominantSeqbyLength |
retrieve majority of sequences accoring to length distribution. |
|
1 |
RetriveNCBIRefbyBlastn |
from the reference genomes(NCBIRef). |
|
1 |
RetriveSeqViaAcc |
Download Gene/genomic sequences from GenBank via accession numbers |
|
1 |
Reverse |
columns in a tabular file |
|
5 |
Reverse Complement |
a MAF file |
|
1 |
Reverse-Complement |
|
|
5 |
Reverse.seqs |
Reverse complement the sequences |
|
5 |
RevertOriginalBaseQualitiesAndAddMateCigar |
revert the original base qualities and add the mate cigar tag |
|
14 |
revertR2orientationInBam |
Revert the mapped orientation of R2 mates in a bam. |
|
1 |
RevertSam |
revert SAM/BAM datasets to a previous state |
|
14 |
revseq |
Reverse and complement a sequence |
|
5 |
rgbcolor2hex |
change rgb color into hex color format. |
|
1 |
RGCCA |
performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals. |
Analysis
Correlation
Visualisation
|
2 |
RhizosphereRatio |
Diversity or population. |
|
1 |
riboPicker |
Easy identification and removal of rRNA-like sequences. |
|
1 |
ribotaper part 1: creation of annotation files |
|
|
4 |
ribotaper part 2: metagene analysis for P-sites definition |
|
|
4 |
ribotaper part 3: ribosome profiling |
|
|
4 |
RmDup |
remove PCR duplicates |
|
5 |
RMSD Analysis |
using Bio3D |
|
2 |
RMSF Analysis |
using Bio3D |
|
2 |
RNA Coverage Filter: |
Select SNVs with specified RNA coverage |
|
1 |
RNA fragment size |
calculates the fragment size for each gene/transcript |
|
8 |
RNA Mapping |
summary based on BLASTN reporter |
|
1 |
RNA STAR |
Gapped-read mapper for RNA-seq data |
Mapping assembly
Sequence alignment
|
19 |
RNA STARSolo |
mapping, demultiplexing and gene quantification for single cell RNA-seq |
Sequence alignment
|
8 |
RNA Structure Prediction |
predict RNA structures with or without experimental constraints from the Reactivity Calculation module |
|
1 |
RNA-seq Rcorrector |
a kmer-based error correction method for RNA-seq data |
|
1 |
RNA/DNA |
converter |
|
5 |
RNA2Dfold |
explore structure space between two reference structures |
|
1 |
RNAaliduplex |
find binding sites of two RNA alignments |
|
1 |
RNAalifold |
Calculate minimum free energy secondary structures and partition function on a multiple alignment file |
|
1 |
RNABOB |
Fast Pattern searching for RNA secondary structures |
|
2 |
RnaChipIntegrator |
Integrated analysis of 'gene' and 'peak' data |
|
3 |
RNAcode |
Analyze the protein coding potential in MSA. |
|
3 |
RNAcofold |
Calculate secondary structures of two RNAs with dimerization |
|
1 |
RNAcommender |
genome-wide recommendation of RNA-protein interactions |
|
2 |
RNAdistance |
Calculate distance between secondary structures of two RNAs |
|
1 |
RNAduplex |
Compute the structure upon hybridization of two RNA strands |
|
1 |
RNAeval |
Calculate energy of RNA sequences with given secondary structure |
|
1 |
RNAfold |
Calculate minimum free energy secondary structures and partition function of RNAs |
|
1 |
RNAheat |
Calculate energies of RNA in a temperature range |
|
1 |
RNAinverse |
Calculate RNA sequence from secondary structure |
|
1 |
RNALalifold |
Calculate locally stable secondary structures for a set of aligned RNAs |
|
1 |
RNALfold |
calculates locally stable secondary structures of RNA |
|
1 |
RNAlien |
Unsupervised covariance model construction from a single input sequence |
|
1 |
RNApaln |
RNA alignment based on sequence base pairing propensities |
|
1 |
RNApdist |
Calculate distances between thermodynamic RNA secondary structure ensembles |
|
1 |
RNAPKplex |
predicts RNA secondary structures including pseudoknots |
|
1 |
RNAplex |
Find targets of a query RNA |
|
1 |
RNAplfold |
predicts RNA secondary structures including pseudoknots |
|
1 |
RNAplot |
Draw RNA Secondary Structures |
|
1 |
rnaQUAST |
A Quality Assessment Tool for De Novo Transcriptome Assemblies |
|
3 |
RNASeq samples quality check |
for transcript quantification |
|
1 |
RNASeq samples quality check |
for transcript quantification |
|
11 |
RNAshapes |
RNA Secondary structure prediction |
|
2 |
RNAsnoop |
Find targets of a query H/ACA snoRNA |
|
1 |
RNAsnp |
Efficient detection of local RNA secondary structure changes induced by SNPs |
|
1 |
rnaSPAdes |
de novo transcriptome assembler |
|
13 |
RNAsubopt |
Calculates suboptimal secondary structures of RNAs |
|
1 |
RNAup |
Calculate the thermodynamics of RNA-RNA interactions |
|
1 |
rnaviralSPAdes |
de novo assembler for transcriptomes, metatranscriptomes and metaviromes |
|
6 |
RNAz |
predicting structurally conserved and thermodynamically stable RNA secondary structures |
|
3 |
RNAz Cluster |
|
|
1 |
RNAz Randomize Aln |
|
|
1 |
RNAz Select Seqs |
|
|
1 |
RNAz windows |
|
|
1 |
RnBeads |
Performs RnBeads analysis for the selected set of |
|
1 |
Roary |
the pangenome pipeline - Quickly generate a core gene alignment from gff3 files |
|
8 |
Rolling window |
over a dataframe (e.g. for data smoothing) |
|
1 |
RootCalibration |
calculate pairwise distance between sampling points. |
|
1 |
RPKM |
of HTS dataframe |
|
1 |
RPKM Count |
calculates raw count and RPKM values for transcript at exon, intron, and mRNA level |
|
4 |
RPKM Saturation |
calculates raw count and RPKM values for transcript at exon, intron, and mRNA level |
|
12 |
RSEM abundance estimation |
run RSEM to estimate transcript abundances |
|
1 |
RSEM calculate expression |
RNA-Seq by Expectation-Maximization |
|
1 |
RSEM prepare reference |
|
|
1 |
RSEM trinity fasta to gene map |
extract transcript to gene map from trinity |
|
1 |
rtsne |
|
|
1 |
Run |
linux command |
|
1 |
Run OpenDUck |
steered molecular dynamics runs |
|
1 |
rxDock cavity definition |
- generate the active site definition needed for rxDock docking |
|
3 |
rxDock docking |
- perform protein-ligand docking with rxDock |
|
4 |
RXLR Motifs |
Find RXLR Effectors of Plant Pathogenic Oomycetes |
|
5 |
SADI services generic caller |
Send any input RDF to any SADI service |
|
1 |
Sailfish |
transcript quantification from RNA-seq data |
|
4 |
SAINT Output to Protein Interaction File |
|
|
1 |
SAINT pre-processing |
|
|
1 |
SAINTexpress |
|
|
1 |
Salmon quant |
Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads |
|
13 |
Salmon quantmerge |
Merge multiple quantification results into a single file |
|
5 |
Salmonella Subtyping |
|
|
2 |
salmonKallistoMtxTo10x |
Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data |
|
3 |
SALSA |
scaffold long read assemblies with Hi-C |
|
5 |
sam-stats |
- Compute statistics from SAM or BAM files |
|
1 |
SAM-to-BAM |
convert SAM to BAM |
|
8 |
sam-to-bam |
converter |
|
1 |
sam-to-bigwig |
converter |
|
1 |
sam-to-qname_sorted.bam |
converter |
|
1 |
sam-to-unsorted.bam |
converter |
|
1 |
SAM/BAM Alignment Summary Metrics |
|
|
2 |
SAM/BAM GC Bias Metrics |
|
|
2 |
SAM/BAM Hybrid Selection Metrics |
for targeted resequencing data |
|
3 |
SAM/BAM to count matrix |
using HTSeq code |
|
1 |
SAM/BAM To Counts |
- Create a digital expression matrix by counting reads aligned to transcripts |
|
1 |
SampComp |
to compare Nanopolished datasets |
|
2 |
Sample Filter |
Remove peaks that fail to appear in x-out-of-n (biological) samples |
|
2 |
Sample SNPs |
: Select a specified number of SNPs, uniformly spaced |
|
2 |
SampleGC |
calculate the GC content of sample. |
|
1 |
SamToFastq |
extract reads and qualities from SAM/BAM dataset and convert to fastq |
|
19 |
Samtools ampliconclip |
clip primer bases from bam files |
|
2 |
samtools BAM to CRAM |
convert BAM alignments to CRAM format |
|
4 |
Samtools calmd |
recalculate MD/NM tags |
|
4 |
Samtools coverage |
computes the depth at each position or region |
|
2 |
Samtools depth |
compute the depth at each position or region |
|
4 |
Samtools fastx |
extract FASTA or FASTQ from alignment files |
|
3 |
Samtools fixmate |
fill mate coordinates, ISIZE and mate related flags |
|
3 |
Samtools flagstat |
tabulate descriptive stats for BAM datset |
|
8 |
Samtools markdup |
marks duplicate alignments |
|
7 |
Samtools merge |
merge multiple sorted alignment files |
|
3 |
samtools mpileup |
multi-way pileup of variants |
|
11 |
Samtools sort |
order of storing aligned sequences |
|
7 |
Samtools split |
BAM dataset on readgroups |
|
5 |
Samtools stats |
generate statistics for BAM dataset |
|
7 |
Samtools view |
- reformat, filter, or subsample SAM, BAM or CRAM |
|
9 |
sansa annotate |
structural variants |
Genetic variation analysis
|
2 |
sarscov2formatter |
|
|
3 |
sarscov2summary |
|
|
1 |
SARTools DESeq2 |
Compare two or more biological conditions in a RNA-Seq framework with DESeq2 |
|
4 |
SARTools edgeR |
Compare two or more biological conditions in a RNA-Seq framework with edgeR |
|
4 |
SaveImages |
or movie files |
|
2 |
Scale Image |
Scales image |
|
3 |
scanMotifGenomeWide |
|
|
1 |
Scanpy ComputeGraph |
to derive kNN graph |
|
16 |
Scanpy FilterCells |
based on counts and numbers of genes expressed |
|
15 |
Scanpy FilterGenes |
based on counts and numbers of cells expressed |
|
15 |
Scanpy FindCluster |
based on community detection on KNN graph |
|
17 |
Scanpy FindMarkers |
to find differentially expressed genes between groups |
|
17 |
Scanpy FindVariableGenes |
based on normalised dispersion of expression |
|
13 |
Scanpy Harmony |
adjust principal components for variables that might introduce batch effect |
|
7 |
Scanpy NormaliseData |
to make all cells having the same total expression |
|
14 |
Scanpy ParameterIterator |
produce an iteration over a defined parameter |
|
5 |
Scanpy PlotEmbed |
visualise cell embeddings |
|
12 |
Scanpy Read10x |
into hdf5 object handled by scanpy |
|
13 |
Scanpy RunPCA |
for dimensionality reduction |
|
14 |
Scanpy RunTSNE |
visualise cell clusters using tSNE |
|
15 |
Scanpy RunUMAP |
visualise cell clusters using UMAP |
|
14 |
Scanpy ScaleData |
to make expression variance the same for all genes |
|
13 |
Scater: Calculate QC metrics |
Computes QC metrics from single-cell expression matrix |
|
4 |
Scater: filter SCE |
with user-defined parameters or PCA |
|
5 |
Scater: normalize SCE |
Compute normalised expression values for SCE |
|
3 |
Scater: PCA plot |
cell-level reduced dimension of a normalised SCE |
|
4 |
Scater: plot expression frequency |
Plot the frequency of expression against the mean expression level for SCE |
|
2 |
Scater: plot library QC |
to visualise library size, feature counts and mito gene expression |
|
4 |
Scater: t-SNE plot |
Produces a t-SNE plot of two components |
|
3 |
Scatterplot |
of two numeric columns |
|
4 |
Scatterplot with ggplot2 |
|
|
10 |
SCEasy convert |
a data object between formats |
|
1 |
scHicAdjustMatrix |
clusters single-cell Hi-C interaction matrices on the raw data |
|
2 |
scHicCluster |
clusters single-cell Hi-C interaction matrices on the raw data |
|
2 |
scHicClusterCompartments |
clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction |
|
2 |
scHicClusterMinHash |
clusters single-cell Hi-C interaction matrices with MinHash dimension reduction |
|
2 |
scHicClusterSVL |
clusters single-cell Hi-C interaction matrices with svl dimension reduction |
|
2 |
scHicConsensusMatrices |
creates per cluster one average matrix |
|
2 |
scHicCorrectMatrices |
correct with KR algorithm single-cell Hi-C interaction matrices |
|
2 |
scHicCreateBulkMatrix |
creates the bulk matrix out of single-cell Hi-C interaction matrices |
|
1 |
scHicDemultiplex |
demultiplexes Nagano 2017 raw fastq files |
|
2 |
scHicInfo |
information about a single-cell scool matrix |
|
2 |
scHicMergeMatrixBins |
change the resolution of the scHi-C matrices |
|
2 |
scHicMergeToMCool |
merge multiple cool files to one mcool file |
|
1 |
scHicMergeToSCool |
merge multiple cool files to one scool file |
|
1 |
scHicNormalize |
normalize single-cell Hi-C interaction matrices to the same read coverage |
|
2 |
scHicPlotClusterProfiles |
plot single-cell Hi-C interaction matrices cluster profiles |
|
2 |
scHicPlotConsensusMatrices |
plot single-cell Hi-C interaction matrices cluster consensus matrices |
|
2 |
scHicQualityControl |
quality control for single-cell Hi-C interaction matrices |
|
2 |
Science Parser |
parse Science paper into json format. |
|
1 |
Scipio |
alignment of proteins on a genome |
|
1 |
Scipio2Apollo |
Transform a Scipio GFF to a WebApollo compliant GFF |
|
1 |
Scoary |
calculates the assocations between all genes in the accessory genome and the traits |
|
1 |
Score docked poses using SuCOS |
- compare shape and feature overlap of docked ligand poses to a reference molecule |
|
4 |
Score_proteins |
Score proteins using test repertoire |
|
1 |
Score_proteins_from_aa_freq |
Score proteins using library frequencies |
|
1 |
scPipe |
- preprocessing pipeline for single cell RNA-seq |
|
4 |
Screen |
a compound against a library using RDKit |
|
2 |
Screen.seqs |
Screen sequences |
|
6 |
SDF sort and filter |
using the sdsort provided with rxDock |
|
3 |
SDF to CML |
|
|
2 |
SDF to Fingerprint |
- extract fingerprints from sdf file metadata |
|
5 |
SDF to InChI |
|
|
2 |
SDF to mol2 |
|
|
2 |
SDF to SMILES |
|
|
2 |
SEACR |
for sparse enrichment analysis |
|
1 |
SEACR |
for sparse enrichment analysis |
|
1 |
Search ChEMBL database |
for compounds which are similar to a SMILES string |
|
6 |
Search GUI |
Perform protein identification using various search engines and prepare results for input to Peptide Shaker |
|
22 |
Search in textfiles |
(grep) |
|
11 |
SearchToLib |
Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data |
|
3 |
Secure Hash / Message Digest |
on a dataset |
|
2 |
segemehl |
short read mapping with gaps |
|
3 |
segmentation-fold |
RNA-Folding including predefined segments including K-turns |
|
4 |
Select |
lines that match an expression |
Filtering
|
3 |
Select |
unique seqs by ids |
|
1 |
Select |
seqs by length |
|
1 |
Select Fasta sequences |
from a file |
|
1 |
Select first |
lines from a dataset |
Filtering
|
4 |
Select first |
lines from a dataset (head) |
|
9 |
Select high quality segments |
|
|
2 |
Select last |
lines from a dataset |
|
2 |
Select last |
lines from a dataset (tail) |
|
9 |
Select populations |
for analysis |
|
1 |
Select random lines |
from a file |
|
2 |
Select samples |
based on sample list,factors,regex and readnums from data frame |
|
1 |
Select Sequences |
Tool to select representative sequences from a multiple sequence alignment. |
|
2 |
Select sequences by ID |
from a tabular file |
|
3 |
Select Taxonomic |
groups from the data frame |
|
1 |
Select uninterrupted STRs |
of a specific column |
|
1 |
Select Variants |
from VCF files |
|
3 |
Select Variants |
from VCF files |
|
1 |
Select_Frequent_OTU |
from a taxonomic OTU reporter |
|
1 |
Select_module |
transform 2D dataframe to Arrays(mxd format) |
|
1 |
Select_OTUs |
with the highest abundant from samples |
|
1 |
Select_OTUs |
from a taxonomic OTU reporter with minimum number of reads |
|
1 |
Select_seqs_by_id |
from a fasta file |
|
1 |
SelectColumn |
select the columns with the value . |
|
1 |
SelectRespondingTaxa |
from a statistic analysis. |
|
1 |
SelectSubgraphbyNode |
from a gml format network. |
|
1 |
SelectTopKOs |
筛选最相近KO,Select the toppest KO. |
|
1 |
SelectTopNByTaxa |
select top n OTUs with highest abundance. |
|
1 |
SEM |
analysis to relationship between datasets. |
|
1 |
Send Mail On Completion |
|
|
1 |
Send to cloud |
|
|
1 |
Sens.spec |
Determine the quality of OTU assignment |
|
6 |
Separate paired and unpaired reads |
from two fastq files |
|
1 |
Separate pgSnp alleles |
into columns |
|
1 |
Seq.error |
assess error rates in sequencing data |
|
5 |
seq2HLA |
HLA genotype and expression from RNA-seq |
|
2 |
Seq2HLA: |
Predict HLA class I and II alleles using Illumina paired-end RNA-seq reads |
|
1 |
Seq2OTU |
generating an OTU table according to Sequence identity. |
|
1 |
SeqClusterByDistance |
number of clusters under different sequence distance. |
|
1 |
SeqKit fx2tab |
convert FASTA/Q to tabular |
|
3 |
SeqKit statistics |
of FASTA/Q files |
|
3 |
SeqLenDistri |
check the length distribution of a fasta seq. |
|
1 |
seqmatchall |
All-against-all comparison of a set of sequences |
|
5 |
seqret |
Reads and writes sequences |
|
5 |
SeqsintoGroups |
based on sequence identity |
|
1 |
seqtk_comp |
get the nucleotide composition of FASTA/Q |
|
6 |
seqtk_cutN |
cut sequence at long N |
|
6 |
seqtk_dropse |
drop unpaired from interleaved Paired End FASTA/Q |
|
6 |
seqtk_fqchk |
fastq QC (base/quality summary) |
|
6 |
seqtk_hety |
regional heterozygosity |
|
6 |
seqtk_listhet |
extract the position of each het |
|
6 |
seqtk_mergefa |
merge two FASTA/Q files |
|
6 |
seqtk_mergepe |
interleave two unpaired FASTA/Q files for a paired-end file |
|
6 |
seqtk_mutfa |
point mutate FASTA at specified positions |
|
6 |
seqtk_randbase |
choose a random base from hets |
|
6 |
seqtk_sample |
random subsample of fasta or fastq sequences |
|
6 |
seqtk_seq |
common transformation of FASTA/Q |
|
6 |
seqtk_subseq |
extract subsequences from FASTA/Q files |
|
6 |
seqtk_trimfq |
trim FASTQ using the Phred algorithm |
|
6 |
Sequence composition |
Count bases or amino-acids |
|
3 |
Sequence Content Trimmer |
trim reads based on certain bases |
|
2 |
Sequence Logo |
generator for fasta (eg Clustal alignments) |
|
2 |
seqwish |
Alignment to variation graph inducer |
|
7 |
Seurat |
- toolkit for exploration of single-cell RNA-seq data |
|
12 |
SFF converter |
|
|
1 |
Sffinfo |
Summarize the quality of sequences |
|
5 |
Shape alignment |
against a database of molecules (Shape-it) |
|
1 |
Sharpen |
|
|
2 |
Shasta |
De novo assembly of long read sequencing data |
|
1 |
Shhh.flows |
Denoise flowgrams (PyroNoise algorithm) |
|
5 |
Shhh.seqs |
Denoise program (Quince SeqNoise) |
|
5 |
shift longitudes |
from netCDF data |
|
1 |
Shovill |
Faster SPAdes assembly of Illumina reads |
|
8 |
Show nucleotide |
distribution in nanopore sequencing reads |
|
2 |
Show quality |
score distribution in nanopore sequencing reads |
|
2 |
Show-Coords |
Parse delta file and report coordinates and other information |
Read mapping
Sequence alignment
|
5 |
showfeat |
Show features of a sequence |
|
5 |
shuffleseq |
Shuffles a set of sequences maintaining composition |
|
5 |
SICER |
Statistical approach for the Identification of ChIP-Enriched Regions |
|
3 |
Sickle |
windowed adaptive trimming of FASTQ data |
|
4 |
SIFT |
predictions of functional sites |
|
1 |
sigcleave |
Reports protein signal cleavage sites |
|
5 |
SignalP 3.0 |
Find signal peptides in protein sequences |
|
4 |
Similarity search |
of fingerprint data sets with chemfp |
|
4 |
Simulate |
Illumina runs |
|
1 |
SINA |
reference based multiple sequence alignment |
|
5 |
SINA aligner |
SILVA Incremental Aligner |
|
1 |
SIRIUS-CSI:FingerID |
is used to identify metabolites using single and tandem mass spectrometry |
|
7 |
sirna |
Finds siRNA duplexes in mRNA |
|
5 |
sistr_cmd |
Salmonella In Silico Typing Resource commandline tool for serovar prediction |
|
3 |
sixgill build |
a metapeptide database from metagenome fastq files |
|
1 |
sixgill filter |
a metapeptide database |
|
1 |
sixgill makefasta |
from a metapeptide database |
|
1 |
sixgill merge |
metapeptide databases |
|
1 |
sixpack |
Display a DNA sequence with 6-frame translation and ORFs |
|
7 |
Skeletonize |
|
|
2 |
skipseq |
Reads and writes sequences, skipping first few |
|
5 |
Slamdunk |
- streamlining SLAM-seq analysis with ultra-high sensitivity |
|
6 |
Slice |
BAM by genomic regions |
|
5 |
Slice Image |
into smaller patches |
|
2 |
Slice MD trajectories |
using the MDTraj package |
|
3 |
Slice VCF |
to get data from selected regions |
|
1 |
SMALT |
maps query reads onto the reference sequences |
|
1 |
SMART |
- Statistical Mitogenome Assembly with Repeats |
|
1 |
SMART2: |
Multi-Sample Statistical Mitogenome Assembly with Repeats |
|
1 |
smi-to-mol |
converter |
|
2 |
smi-to-smi |
converter |
|
2 |
SmileFinder |
- detect signatures of positive selection in genomes |
|
1 |
SMILES to CML |
|
|
2 |
SMILES to InChI |
|
|
2 |
SMILES to MOL2 |
|
|
2 |
SMILES to SDF |
|
|
2 |
smina |
Scoring and Minimization with AutoDock Vina |
|
1 |
Smooth |
|
|
2 |
Smudgeplot |
inference of ploidy and heterozygosity structure using whole genome sequencing |
|
1 |
SNAP |
gene prediction |
|
1 |
sniffles |
Structural variation caller using third generation sequencing |
|
1 |
snippy |
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. |
|
11 |
snippy-clean_full_aln |
Replace any non-standard sequence characters in snippy 'core.full.aln' file. |
|
4 |
snippy-core |
Combine multiple Snippy outputs into a core SNP alignment |
|
10 |
SNP distance matrix |
Compute distance in SNPs between all sequences in a FASTA file |
|
2 |
snp2gcoords |
SNP to Genomic Coordinates |
|
1 |
SnpEff build: |
database from Genbank or GFF record |
|
13 |
SnpEff chromosome-info: |
list chromosome names/lengths |
|
8 |
SnpEff databases: |
list available databases |
|
13 |
SnpEff download: |
download a pre-built database |
|
13 |
SnpEff eff: |
annotate variants |
|
11 |
SnpEff eff: |
annotate variants for SARS-CoV-2 |
|
1 |
SnpEff Ensembl CDS |
Report Variant coding sequence changes for SnpEffects |
|
1 |
SnpEff to Peptide fasta |
to create a Search DB fasta for variant SAP peptides |
|
1 |
snpFreq |
significant SNPs in case-control data |
|
2 |
SNPGeneGlobalLDChecker |
Linkage disequilibrium in SNP/gene pairs |
|
1 |
SnpSift Annotate |
SNPs from dbSnp |
|
9 |
SnpSift CaseControl |
Count samples are in 'case' and 'control' groups. |
|
9 |
SnpSift dbNSFP |
Add annotations from dbNSFP or similar annotation DBs |
|
4 |
SnpSift dbNSFP |
Add Annotations from dbNSFP and similar annotation DBs |
|
2 |
SnpSift Extract Fields |
from a VCF file into a tabular file |
|
7 |
SnpSift Filter |
Filter variants using arbitrary expressions |
|
9 |
SnpSift GeneSets |
Annotating GeneSets, such as Gene Ontology, KEGG, Reactome |
|
4 |
SnpSift Intervals |
Filter variants using intervals |
|
9 |
SnpSift rmInfo |
remove INFO field annotations |
|
8 |
SnpSift Variant Type |
Annotate with variant type |
|
8 |
SnpSift vcfCheck |
basic checks for VCF specification compliance |
|
8 |
SOAPDenovo |
assembler of RNA-seq. |
|
1 |
SOAPdenovo1 |
|
|
1 |
SOAPdenovo2 |
|
|
1 |
SOAPfilter |
- removes reads with artefacts |
|
1 |
socru |
Calculate the order and orientation of complete bacterial genomes |
|
1 |
Somatic SNV Filter: |
Select somatic calls made by the CCCP pipeline |
|
1 |
Sort |
data in ascending or descending order |
Sorting
|
3 |
Sort |
data in ascending or descending order |
|
11 |
Sort a row |
according to their columns |
|
12 |
Sort assembly |
|
|
5 |
Sort by chromosome |
Sort various tabular files according to the chromosome and start coordinate |
|
1 |
Sort Column Order |
by heading |
|
1 |
Sort.seqs |
put sequences in different files in the same order |
|
6 |
Sort_Samples |
of a dataframes according treatments or all samples |
|
1 |
SortSam |
sort SAM/BAM dataset |
|
14 |
SPAdes |
assemble contigs with the packages of SPAdes verion 3.14 |
|
1 |
SPAdes |
genome assembler for genomes of regular and single-cell projects |
Genome assembly
|
16 |
SPAdes stats |
coverage vs. length plot |
|
1 |
Spaln: align cDNA or Protein to genome |
Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. |
|
5 |
SPARQL Import |
Import data from a SPARQL Endpoint |
|
1 |
Sparse Matrix Functions |
for manipulating 2-D Scipy sparse numeric data |
|
11 |
Spatial coordinates anonymization |
without loss of the spatial relationships |
|
1 |
SpearmanNet |
for analyze microbial network |
|
1 |
SpearmanNet2 |
construct network without data transformation. |
|
1 |
Specify Individuals |
: Define a collection of individuals from a gd_snp dataset |
|
3 |
Spectrophores search |
- similarity search based on 1D chemical features |
|
5 |
Spectrophores(TM) search: |
similarity search based on 1D chemical features |
|
2 |
Spider Clouds |
plot dots according to their affinity to treatments.(gc_ding). |
|
1 |
Spider Plot |
of data according to known factors. |
|
1 |
Split |
BAM datasets on variety of attributes |
|
3 |
Split |
a merged HUMAnN table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Split |
BAM datasets on variety of attributes |
|
3 |
Split |
a HUMAnN2 generated table |
|
4 |
Split a HUMAnN table |
into 2 tables (one stratified and one unstratified) |
Nucleic acid sequence analysis
Phylogenetic analysis
|
3 |
Split BAM on ReadGroups |
|
|
1 |
Split Dataset |
into training and test subsets |
|
6 |
Split Fasta |
files into a collection |
|
3 |
Split Fastq |
into samples |
|
1 |
Split file |
according to the values of a column |
|
4 |
Split file |
to dataset collection |
|
7 |
Split Labelmap |
|
|
1 |
Split MAF blocks |
by Species |
|
1 |
Split objects |
Split binary image by using watershed |
|
1 |
Split paired end reads |
|
|
1 |
Split stratified table |
|
|
3 |
Split.abund |
Separate sequences into rare and abundant groups |
|
5 |
Split.groups |
Generates a fasta file for each group |
|
5 |
split_scores |
splits the output of threshold3 |
|
1 |
SplitFile10x |
Split file in 10 |
|
1 |
SplitFile4x |
Split file in 4 |
|
1 |
SplitFileUpTo10x |
Split file in 2-10 |
|
1 |
splitter |
Split a sequence into (overlapping) smaller sequences |
|
5 |
Spot Detection |
in a 2D image (sequence) |
|
3 |
SpoTyping |
fast and accurate in silico Mycobacterium spoligotyping from sequence reads |
|
1 |
SPRING Cross |
reference builder |
|
1 |
SPRING Map |
with BLAST |
|
1 |
SPRING MCC |
plot generator |
|
1 |
SPRING Min-Z |
filter operation |
|
1 |
SPRING Model |
complex structures |
|
1 |
SPRING Model-All |
complex structures |
|
1 |
SpyBOAT |
wavelet analyzes image stacks |
|
2 |
SQLite to tabular |
for SQL query |
|
3 |
sRNAPipe |
In-depth study of small RNA |
|
4 |
SSAKE |
short DNA sequences assembler |
|
1 |
ssHMM |
- RNA sequence-structure motif finder |
|
1 |
SSPACE |
scaffolder |
|
1 |
Stacking Ensembles |
builds stacking, voting ensemble models with numerous base options |
|
8 |
STACKS : assemble read pairs by locus |
Run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers |
|
1 |
STACKS : De novo map |
Run the STACKS denovo_map.pl wrapper |
|
1 |
STACKS : genotypes |
Run the STACKS genotypes program |
|
1 |
STACKS : populations |
Run the STACKS populations program |
|
1 |
STACKS : Prepare population map file |
for STACKS denovomap and refmap |
|
1 |
STACKS : Process radtags |
Run the STACKS cleaning script |
|
1 |
STACKS : Reference map |
Run the STACKS ref_map.pl wrapper |
|
1 |
Stacks2: clone filter |
Identify PCR clones |
|
8 |
Stacks2: cstacks |
Generate catalog of loci |
|
8 |
Stacks2: de novo map |
the Stacks pipeline without a reference genome (denovo_map.pl) |
|
8 |
Stacks2: gstacks |
Call variants, genotypes and haplotype |
|
8 |
Stacks2: kmer filter |
Identify PCR clones |
|
8 |
Stacks2: populations |
Calculate population-level summary statistics |
|
8 |
Stacks2: process radtags |
the Stacks demultiplexing script |
|
8 |
Stacks2: process shortreads |
fast cleaning of randomly sheared genomic or transcriptomic data |
|
8 |
Stacks2: reference map |
the Stacks pipeline with a reference genome (ref_map.pl) |
|
8 |
Stacks2: sstacks |
Match samples to the catalog |
|
8 |
Stacks2: tsv2bam |
Sort reads by RAD locus |
|
8 |
Stacks2: ustacks |
Identify unique stacks |
|
8 |
Stacks: assemble read pairs by locus |
run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers |
|
6 |
Stacks: clone filter |
Identify PCR clones |
|
2 |
Stacks: cstacks |
build a catalogue of loci |
|
5 |
Stacks: de novo map |
the Stacks pipeline without a reference genome (denovo_map.pl) |
|
5 |
Stacks: genotypes |
analyse haplotypes or genotypes in a genetic cross ('genotypes' program) |
|
5 |
Stacks: populations |
analyze a population of individual samples ('populations' program) |
|
5 |
Stacks: process radtags |
the Stacks demultiplexing script |
|
5 |
Stacks: pstacks |
find stacks from short reads mapped to a reference genome |
|
5 |
Stacks: reference map |
the Stacks pipeline with a reference genome (ref_map.pl) |
|
5 |
Stacks: rxstacks |
make corrections to genotype and haplotype calls |
|
5 |
Stacks: sstacks |
match stacks to a catalog |
|
4 |
Stacks: statistics |
on stacks found for multiple samples |
|
2 |
Stacks: ustacks |
align short reads into stacks |
|
5 |
Standardize SD-files |
using RDKit |
|
2 |
STAR-Fusion |
detect fusion genes in RNA-Seq data |
|
4 |
staramr |
Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes. |
|
11 |
sTarPicker |
sTarPicker (ViennaRNA 2.3.4) |
|
1 |
Starting Modules |
load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups) |
|
2 |
stat |
- Extract information from GAGE output |
|
1 |
Statistic image |
mark statistic result in a manner of heatmap style. |
|
1 |
Statistic2BiNetwork |
construct a network based on statistic analysis |
|
1 |
StatisticNet |
generate an network based on statistic analysis |
|
1 |
Statistics on presence-absence |
of a numeric variable |
|
1 |
Stitch Gene blocks |
given a set of coding exon intervals |
|
4 |
Stitch MAF blocks |
given a set of genomic intervals |
|
1 |
STR detection |
for short read, reference, and mapped data |
|
1 |
Strelka Germline |
small variant caller for germline variation in small cohorts |
|
2 |
Strelka Somatic |
small variant caller for somatic variation in tumor/normal sample pairs |
|
1 |
StringTie |
transcript assembly and quantification |
|
17 |
StringTie merge |
transcripts |
|
11 |
Strip-it |
extracts predefined scaffolds from molecules |
|
1 |
Structure |
using multi-locus genotype data to investigate population structure |
|
2 |
Sub-sample sequences files |
e.g. to reduce coverage |
|
4 |
Sub.sample |
Create a sub sample |
|
5 |
Subseq of fasta |
retrieve subseqs from a fasta files |
|
1 |
Subset |
columns from a VCF dataset |
|
1 |
Substructure Search |
of fingerprint data sets |
|
2 |
Substructure Search |
of fingerprint data sets |
|
5 |
Subtract |
the intervals of two datasets |
Filtering
|
6 |
Subtract Whole Dataset |
from another dataset |
|
2 |
subtract_control_from_test |
subtract control from test |
|
1 |
Sum up Tax |
from the data frame |
|
1 |
Summarize taxonomy |
|
|
1 |
Summary Report Generator: |
Collect statistics from a CCCP log file |
|
1 |
Summary Statistics |
for any numerical column |
|
3 |
Summary.qual |
Summarize the quality scores |
|
6 |
Summary.seqs |
Summarize the quality of sequences |
|
5 |
Summary.shared |
Summary of calculator values for OTUs |
|
5 |
Summary.single |
Summary of calculator values for OTUs |
|
6 |
Summary.tax |
Assign sequences to taxonomy |
|
5 |
supermatcher |
Match large sequences against one or more other sequences |
|
5 |
Support vector machines (SVMs) |
for classification |
|
12 |
Switch axis coordinates |
Switches the axes of an image and flips the y axis. |
|
1 |
syco |
Synonymous codon usage Gribskov statistic plot |
|
5 |
T Test for Two Samples |
|
|
2 |
T-Coffee |
multiple sequence alignment |
|
3 |
Table |
generator based on mapped |
|
1 |
Table Compute |
computes operations on table data |
|
4 |
Table Merge |
Merging dataMatrix with a metadata table |
|
2 |
Table Recalibration |
on BAM files |
|
1 |
Table to GFF3 |
|
|
2 |
TableJoiner |
Join two unsorted tables |
|
1 |
Tabular to CSV |
|
|
1 |
Tabular to FASTQ |
converter |
Conversion
|
5 |
tabular-to-csv |
converter |
|
1 |
Tabular-to-FASTA |
converts tabular file to FASTA format |
|
2 |
tac |
reverse a file (reverse cat) |
|
9 |
Tadarida data cleaner |
clean data from animal detection on acoustic recordings |
|
1 |
Tadarida data cleaner |
clean data from animal detection on acoustic recordings |
|
1 |
Tadarida identifications integration |
Integrate identifications from animal detection on acoustic recordings |
|
1 |
Tadarida identifications validation |
Integrate identifications from animal detection on acoustic recordings |
|
1 |
Tag pileup frequency |
|
|
3 |
TakeABreak |
is a tool that can detect inversion breakpoints directly from raw NGS reads |
|
3 |
tar |
add files to archive |
|
1 |
tar-to-directory |
converter |
|
2 |
TargetFinder |
plant small RNA target prediction tool |
Sequence alignment
|
2 |
TaxaLists |
of data frame |
|
1 |
Taxaotureporter2LeFse |
split the subspecies column into species . |
|
1 |
Taxonomic OTU reporter |
generating TOR based on fasta sequences(No barcode and primer regions,proper names:Sample_(one letter for replicate)numbers e.g. Org_a1179. |
|
1 |
Taxonomy-to-Krona |
convert a mothur taxonomy file to Krona input format |
|
2 |
Taylor-Butina clustering |
of molecular fingerprints |
|
5 |
TB Variant Filter |
M. tuberculosis H37Rv VCF filter |
|
4 |
TB Variant Report |
- generate HTML report from SnpEff annotated M.tb VCF(s) |
|
3 |
TB-Profiler Profile |
Infer strain types and drug resistance markers from sequences |
|
15 |
tbl2tbl |
Convert among table formats |
|
1 |
tblsubmerge |
Denormalize table |
|
1 |
tblsubsplit |
Normalize table |
|
1 |
tcode |
Fickett TESTCODE statistic to identify protein-coding DNA |
|
5 |
TD: |
Tag distance analysis of duplex tags |
|
3 |
Temporal trend indicator |
using GlmmTMB or GAM models |
|
2 |
TEtranscripts |
annotates reads to genes and transposable elements |
|
4 |
TETyper |
Transposable Element Typer |
|
3 |
Text reformatting |
with awk |
|
13 |
Text transformation |
with sed |
|
11 |
Text2file |
copy the content in the text area to file |
|
1 |
textsearch |
Search sequence documentation. Slow, use SRS and Entrez! |
|
5 |
Thermo |
RAW file converter |
|
9 |
Thread nucleotides onto a protein alignment (back-translation) |
Gives a codon aware alignment |
|
5 |
threshold3 |
calculate threshold, scores1 and 3 |
|
1 |
threshold_and_scores |
threshold_and_scores |
|
1 |
Tile |
tiles images together to form large montage images |
|
2 |
tmap |
Displays membrane spanning regions |
|
5 |
TMHMM 2.0 |
Find transmembrane domains in protein sequences |
|
5 |
Tn5Gaps |
- determine essential genes |
|
3 |
TN93 |
compute distances between aligned sequences |
|
3 |
TN93 Cluster |
sequences that lie within a specific distance of each other |
|
2 |
TN93 Filter |
- remove sequences from a reference that are within a given distance of of a cluster |
|
2 |
To categorical |
Converts a class vector (integers) to binary class matrix |
|
2 |
toolfactory |
Scripts into tools |
|
1 |
TopHat |
Gapped-read mapper for RNA-seq data |
|
9 |
Tophat for Illumina |
Find splice junctions using RNA-seq data |
|
2 |
Tophat Stats PE |
Calculate mapping statistics from Tophat BAM files. |
|
1 |
TrackObjects |
tracking objects throughout sequential frames of a series of images |
|
2 |
tracy Align |
chromatogram to a FASTA reference |
|
1 |
tracy Assemble |
genomic region from tiled, overlapping Sanger Chromatogram trace files |
|
1 |
tracy Basecall |
from Sanger chromatogram tracefile |
|
1 |
tracy Decompose |
heterozygous mutations (and call variants) |
|
1 |
Train Augustus |
ab-initio gene predictor |
|
5 |
Train SNAP |
ab-initio gene predictor |
|
1 |
Train, Test and Evaluation |
fit a model using part of dataset and evaluate using the rest |
|
7 |
Trajectory select and merge |
- select specific molecules and merge multiple trajectories. |
|
3 |
tranalign |
Align nucleic coding regions given the aligned proteins |
|
5 |
TranOpenron |
Retrieve operon using draft genome and transcriptomics. |
|
1 |
Transcript Integrity Number |
evaluates RNA integrity at a transcript level |
|
8 |
Transcript start detection |
|
|
1 |
Transcript stop detection |
|
|
1 |
transcriptsToOrfs |
Trinity Transcripts to Candidate Peptides |
|
1 |
TransDecoder |
finds coding regions within transcripts |
|
7 |
transeq |
Translate nucleic acid sequences |
|
5 |
Transformation |
Transforms the dataMatrix intensity values |
|
1 |
Translate |
DNA sequences into AA. |
|
1 |
Translate BED Sequences |
3 frame translation of BED augmented with a sequence column |
|
1 |
Translate BED transcripts |
cDNA in 3frames or CDS |
|
1 |
Transpose |
rows/columns in a tabular file |
|
5 |
Transpose_tabular |
file |
|
1 |
TransTermHP |
finds rho-independent transcription terminators in bacterial genomes |
|
2 |
Tree.shared |
Generate a newick tree for dissimilarity among groups |
|
5 |
TreeBeST best |
Generate a phylogenetic tree using CDS alignment and species tree |
|
2 |
TRIC |
integrates information from all available runs via a graph-based alignment strategy |
|
1 |
Trim |
leading or trailing characters |
|
2 |
Trim Galore! |
Quality and adapter trimmer of reads |
|
9 |
Trim sequences |
|
|
5 |
Trim.flows |
partition by barcode, trim to length, cull by length and mismatches |
|
5 |
Trim.seqs |
Trim sequences - primers, barcodes, quality |
|
5 |
trimest |
Trim poly-A tails off EST sequences |
|
5 |
Trimmomatic |
flexible read trimming tool for Illumina NGS data |
Sequence trimming
|
15 |
TrimN |
|
|
1 |
trimseq |
Trim ambiguous bits off the ends of sequences |
|
5 |
Trinity |
de novo assembly of RNA-Seq data |
|
14 |
Trinity |
De novo assembly of RNA-Seq data Using Trinity |
|
1 |
Trinity read normalization |
Pre-process RNA-seq data to reduce coverage of highly covered areas |
|
1 |
Trinotate |
functional transcript annotation |
|
4 |
tRNA and tmRNA |
prediction (Aragorn) |
|
3 |
tRNA prediction |
(tRNAscan) |
|
2 |
tRNAscanSE |
searching for tRNA genes in genomic(DNA) sequences. |
|
1 |
Trycycler cluster |
cluster the contigs of your input assemblies into per-replicon groups |
Genome assembly
|
4 |
Trycycler consensus |
generate a consensus contig sequence for each cluster |
Genome assembly
|
4 |
Trycycler partition |
assign the reads to the clusters |
Genome assembly
|
4 |
Trycycler reconcile/msa |
reconcile the contigs within each cluster and perform a multiple sequence alignment |
Genome assembly
|
4 |
Trycycler subsample |
make a maximally-independent read subsets of an appropiate depth for your genome |
Genome assembly
|
4 |
twoBitToFa |
Convert all or part of .2bit file to FASTA |
|
3 |
twofeat |
Finds neighbouring pairs of features in sequences |
|
5 |
tximport |
Summarize transcript-level estimates for gene-level analysis |
|
3 |
ublast |
Compare query sequences to database |
|
1 |
uc2fastax |
Generate Fasta file from UC file |
|
1 |
UC2list |
convert a uc(10 columns)into 2column lists |
|
1 |
Uchime |
Detecting chimeric sequences with two or more segments. |
|
1 |
uclust |
Cluster sequences by similarity |
|
1 |
uclust_composition |
Create a table of cluster composition by barcode |
|
1 |
UCSC BLAT Alignment Tool |
Standalone blat sequence search command line tool |
|
3 |
UCTaxa2OTUreporter |
construct taxonomic OTU reporter using ucfile and taxa assignment |
|
1 |
UMI-tools count |
performs quantification of UMIs from BAM files |
|
9 |
UMI-tools deduplicate |
Extract UMI from fastq files |
|
6 |
UMI-tools extract |
Extract UMI from fastq files |
|
12 |
UMI-tools group |
Extract UMI from fastq files |
|
8 |
UMI-tools whitelist |
Extract cell barcodes from FASTQ files |
|
8 |
Unfold |
columns from a table |
|
11 |
Unified Genotyper |
SNP and indel caller |
|
3 |
Unified Genotyper |
SNP and indel caller |
|
1 |
unifrac.unweighted |
Describes whether two or more communities have the same structure |
|
5 |
unifrac.weighted |
Describes whether two or more communities have the same structure |
|
5 |
union |
Reads sequence fragments and builds one sequence |
|
5 |
Unipept |
retrieve taxonomy for peptides |
|
6 |
UniProt |
download proteome as XML or fasta |
|
6 |
UniProt |
ID mapping and retrieval |
|
4 |
Unique |
occurrences of each record |
|
1 |
Unique |
occurrences of each record |
|
9 |
Unique lines |
assuming sorted input file |
|
11 |
Unique.seqs |
Return unique sequences |
|
5 |
unique_line |
remove duplicate lines |
|
1 |
Uniseqs |
get unique seqs from a fasta file. |
|
1 |
Univariate |
Univariate statistics |
|
2 |
Unpack pathway abundances |
to show the genes for each |
Nucleic acid sequence analysis
Phylogenetic analysis
|
3 |
Unpack pathway abundances to show genes included |
|
|
3 |
unsorted.bam-to-bigwig |
converter |
|
1 |
untar |
extract files from archive |
|
1 |
Unzip |
Unzip file |
|
1 |
UPGMA cluster |
analysis based on a dist matrix |
|
1 |
Upload File |
from your computer |
Query and retrieval
|
3 |
UpSet diagram |
of intersection of genomic regions or list sets |
|
4 |
Use Consequence 2 to calculate detectability |
Tool for calculating detectability in LCMS in a set of peptides |
|
1 |
usearch sort |
Sort sequences by decreasing length |
|
1 |
UShER |
ultrafast sample placement on existing trees |
Phylogenetic inference (from molecular sequences)
|
1 |
UShER matUtils |
analyze, edit, and manipulate mutation annotated tree files |
Phylogenetic inference (from molecular sequences)
|
1 |
VALET |
to detect mis-assemblies in metagenomic assemblies |
|
1 |
Validate FASTA Database |
|
|
1 |
Validate Variants |
|
|
3 |
Validate Variants |
|
|
1 |
ValidateSamFile |
assess validity of SAM/BAM dataset |
|
15 |
VarDict |
calls SNVs and indels for tumor-normal pairs |
|
4 |
Variables exploration |
Shows interaction, correlation, colinearity, produces a PCA and computes VIF for biodiversity abundance data |
|
1 |
Variant Annotator |
|
|
3 |
Variant Annotator |
|
|
1 |
Variant Annotator |
process variant counts |
|
3 |
Variant Filtration |
on VCF files |
|
3 |
Variant Filtration |
on VCF files |
|
1 |
Variant Frequency Plot |
Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data |
Aggregation
|
4 |
Variant Recalibrator |
|
|
3 |
Variant Recalibrator |
|
|
2 |
Variation of community composition within treatments |
based on pairwised distances. |
|
1 |
Variation_Partion |
of community composition using different sets of explaining matrixs |
|
1 |
VarScan |
for variant detection |
|
2 |
VarScan copynumber |
Determine relative tumor copy number from tumor-normal pileups |
|
4 |
VarScan mpileup |
for variant detection |
|
4 |
VarScan somatic |
Call germline/somatic and LOH variants from tumor-normal sample pairs |
|
9 |
VarScan Somatic (Native Output) |
somatic mutation caller for cancer genomics |
|
1 |
VarScan Somatic (VCF Output) |
somatic mutation caller for cancer genomics |
|
1 |
VCF Generator: |
Convert list of SNVs in CCCP output format to VCF |
|
1 |
VCF to MAF Custom Track |
for display at UCSC |
|
2 |
VCF to pgSnp |
Convert from VCF to pgSnp format |
|
1 |
VCF to VariantDB |
|
|
2 |
VCF-BEDintersect: |
Intersect VCF and BED datasets |
|
5 |
vcf-to-bgzip |
converter |
|
2 |
vcf-to-bigwig |
converter |
|
1 |
vcf-to-tabix |
converter |
|
2 |
VCF-VCFintersect: |
Intersect two VCF datasets |
|
5 |
VCF2Dint |
Conversion from VCF to Dintegrator input format |
|
1 |
vcf_bgzip-to-tabix |
converter |
|
2 |
VCFaddinfo: |
Adds info fields from the second dataset which are not present in the first dataset |
|
5 |
VcfAllelicPrimitives: |
Split alleleic primitives (gaps or mismatches) into multiple VCF lines |
|
5 |
vcfanno |
VCF annotation |
|
2 |
VCFannotate: |
Intersect VCF records with BED annotations |
|
5 |
VCFannotateGenotypes: |
Annotate genotypes in a VCF dataset using genotypes from another VCF dataset |
|
5 |
VCFbreakCreateMulti: |
Break multiple alleles into multiple records, or combine overallpoing alleles into a single record |
|
5 |
VCFcheck: |
Verify that the reference allele matches the reference genome |
|
5 |
VCFcombine: |
Combine multiple VCF datasets |
|
6 |
VCFcommonSamples: |
Output records belonging to samples common between two datasets |
|
5 |
VCFdistance: |
Calculate distance to the nearest variant |
|
5 |
VCFfilter: |
filter VCF data in a variety of attributes |
|
8 |
VCFfixup: |
Count the allele frequencies across alleles present in each record in the VCF file |
|
5 |
VCFflatten: |
Removes multi-allelic sites by picking the most common alternate |
|
5 |
VCFgenotype-to-haplotype: |
Convert genotype-based phased alleles into haplotype alleles |
|
5 |
VCFgenotypes: |
Convert numerical representation of genotypes to allelic |
|
5 |
VCFhetHomAlleles: |
Count the number of heterozygotes and alleles, compute het/hom ratio |
|
5 |
VCFleftAlign: |
Left-align indels and complex variants in VCF dataset |
|
5 |
VCFprimers: |
Extract flanking sequences for each VCF record |
|
5 |
VCFrandomSample: |
Randomly sample sites from VCF dataset |
|
5 |
VCFselectsamples: |
Select samples from a VCF dataset |
|
5 |
VCFsort: |
Sort VCF dataset by coordinate |
|
6 |
VCFtoTab-delimited: |
Convert VCF data into TAB-delimited format |
|
6 |
vectorstrip |
Strips out DNA between a pair of vector sequences |
|
5 |
Vegan Diversity |
index |
|
3 |
Vegan Fisher Alpha |
index |
|
3 |
Vegan Rarefaction |
curve and statistics |
|
3 |
velvet |
|
|
1 |
velvetg |
Velvet sequence assembler for very short reads |
De-novo assembly
Formatting
|
6 |
velveth |
Prepare a dataset for the Velvet velvetg Assembler |
De-novo assembly
Formatting
|
6 |
VelvetOptimiser |
Automatically optimize Velvet assemblies |
|
5 |
Venn |
Generate Venn diagrams for groups |
|
5 |
Venn Diagram |
from lists |
|
6 |
vennplot |
for different samples(max 5) |
|
1 |
vg convert |
|
|
1 |
vg deconstruct |
construct a dynamic succinct variation graph |
|
2 |
vg view |
|
|
2 |
VINA Docking |
tool to perform protein-ligand docking with Autodock Vina |
|
5 |
Violin plot w ggplot2 |
|
|
8 |
Visceral |
Evaluate Segmentation |
|
1 |
Visualisation |
of compounds |
|
1 |
Visualisation |
of compounds |
|
5 |
Visualize |
the optimal scoring subnetwork |
|
2 |
Visualize with Krona |
Visualise any hierarchical data |
|
1 |
Volcano Plot |
create a volcano plot |
Visualisation
|
5 |
VSearch alignment |
|
Chimera detection
Sequence clustering
Sequence masking
|
6 |
VSearch chimera detection |
|
Chimera detection
Sequence clustering
Sequence masking
|
6 |
VSearch clustering |
|
Chimera detection
Sequence clustering
Sequence masking
|
7 |
VSearch dereplication |
|
Chimera detection
Sequence clustering
Sequence masking
|
7 |
VSearch masking |
|
Chimera detection
Sequence clustering
Sequence masking
|
6 |
VSearch search |
|
Chimera detection
Sequence clustering
Sequence masking
|
6 |
VSearch shuffling |
|
Chimera detection
Sequence clustering
Sequence masking
|
6 |
VSearch sorting |
|
Chimera detection
Sequence clustering
Sequence masking
|
7 |
vsearch_chimera |
remove chimera sequences from the fasta either by denovo or by references |
|
1 |
vsearch_cluster |
cluster DNA sequences into different groups based on similarity. |
|
1 |
vsearch_derep |
remove replicated sequences |
|
1 |
vsearch_search |
find similar sequences from a database fasta file. |
|
1 |
VT normalize |
normalizes variants in a VCF file |
|
1 |
W4m Data Subset |
Filter W4m data by values or metadata |
|
9 |
Walnut |
PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data |
|
3 |
water |
Smith-Waterman local alignment |
|
5 |
Watershed segmentation |
of binary image |
|
2 |
Wavelet variance |
using Discrete Wavelet Transfoms |
|
3 |
Weeder2 |
Motif discovery in sequences from coregulated genes of a single species |
|
3 |
wig-to-bigwig |
converter |
|
1 |
Wig/BedGraph-to-bigWig |
converter |
|
2 |
Wiggle to Interval |
|
|
2 |
Wiggle-to-Interval |
converter |
|
2 |
Winnowmap |
a mapping tool optimized for repetitive sequences |
Sequence alignment
|
3 |
wobble |
Wobble base plot |
|
5 |
WoLF PSORT |
Eukaryote protein subcellular localization prediction |
|
4 |
wordcount |
Counts words of a specified size in a DNA sequence |
|
5 |
WordFreq |
analyses of inputed text |
|
1 |
wordmatch |
Finds all exact matches of a given size between 2 sequences |
|
5 |
XChem TransFS pose scoring |
using deep learning |
|
3 |
xcms adjustRtime (retcor) |
Retention Time Correction |
|
7 |
xcms fillChromPeaks (fillPeaks) |
Integrate areas of missing peaks |
|
7 |
xcms findChromPeaks (xcmsSet) |
Chromatographic peak detection |
|
8 |
xcms findChromPeaks Merger |
Merge xcms findChromPeaks RData into a unique file to be used by group |
|
5 |
xcms get a sampleMetadata file |
which need to be filled with extra information |
|
3 |
xcms groupChromPeaks (group) |
Perform the correspondence, the grouping of chromatographic peaks within and between samples. |
|
8 |
xcms plot chromatogram |
Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) |
|
5 |
xcms process history |
Create a summary of XCMS analysis |
|
8 |
xcms refineChromPeaks (refine) |
Remove or merge chromatographic peaks based on specific criteria. |
|
1 |
XCos |
scoring |
|
2 |
XLS sheet to Tabular |
|
|
1 |
xmlstarlet |
convert a metadata XML file in one standard to another |
|
1 |
XPath |
compute xpath expressions on XML data |
|
2 |
xtc-to-dcd |
converter |
|
1 |
YAHS |
yet another HI-C scaffolding tool |
|
4 |
zerone |
|
|
1 |
Zip |
and name files |
|
2 |
zonal statistics |
over each area |
|
1 |