AEGeAn CanonGFF3 |
pre-process GFF3 files, removing all features not directly related to protein-coding genes |
Genome annotation
|
1 |
'FeatureStein' fragment overlay scoring |
feature overlay scoring |
|
1 |
2D Feature Extraction |
Feature Extraction |
|
3 |
aaChanges |
amino-acid changes caused by a set of SNPs |
|
2 |
ab1 to FASTQ converter |
|
|
1 |
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 |
ABySS |
de novo sequence assembler |
|
9 |
AccurateMassSearch |
Match MS signals to molecules from a database by mass. |
|
5 |
Adapt an elastic transformation |
to a new image size with bUnwarpJ |
|
2 |
AdapterRemoval: remove adapter sequences |
from HTS data |
|
1 |
Add column |
to an existing dataset |
Editing
|
2 |
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 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 |
AddCommentsToBam |
add comments to BAM dataset |
|
14 |
Adding New Topology Information |
to a GROMACS topology file |
|
1 |
AdditiveSeries |
Computes an additive series to quantify a peptide in a set of samples. |
|
4 |
AddOrReplaceReadGroups |
add or replaces read group information |
|
14 |
Adjust threshold |
of binary image |
|
2 |
Admixture |
: Map genomic intervals resembling specified source populations |
|
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 |
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 |
Alchemical Analysis |
Analysis of alchemical free energy calculations |
|
1 |
ALDEx2 |
differential abundance analysis |
|
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 |
|
12 |
Align Samples |
- Align peaks across Peaklists |
|
2 |
Align sequences |
to a reference using a codon alignment algorithm |
|
6 |
Align sequences |
using a variety of alignment methods (align_seqs) |
|
2 |
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 |
alignmentsieve |
Filter BAM/CRAM files according to specified parameters |
|
7 |
alimask |
append modelmask line to a multiple sequence alignments |
|
7 |
Alleyoop |
- post-processing and QC of Slamdunk analyses |
|
5 |
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 |
ampvis2 alpha diversity |
|
|
1 |
ampvis2 boxplot |
|
|
1 |
ampvis2 core community analysis |
|
|
1 |
ampvis2 export fasta |
|
|
1 |
ampvis2 frequency plot |
|
|
1 |
ampvis2 heatmap |
|
|
1 |
ampvis2 load |
|
|
1 |
ampvis2 merge ampvis2 data sets |
|
|
1 |
ampvis2 merge replicates |
|
|
1 |
ampvis2 octave plot |
|
|
1 |
ampvis2 ordination plot |
|
|
1 |
ampvis2 OTU network plot |
|
|
1 |
ampvis2 rank abundance plot |
|
|
1 |
ampvis2 rarefaction curve |
|
|
1 |
ampvis2 set metadata |
types |
|
1 |
ampvis2 subset data |
by taxonomy |
|
1 |
ampvis2 subset samples |
by sample metadata |
|
1 |
ampvis2 timeseries plot |
|
|
1 |
ampvis2 venn diagram |
|
|
1 |
Analyze particles |
of binary image |
|
2 |
Analyze skeleton |
|
|
2 |
Analyze statistical significance of sample groupings |
using distance matrices (compare_categories) |
|
2 |
Ancestry |
: Characterize ancestries w.r.t. inferred ancestral populations |
|
2 |
ANCOM-BC |
differential abundance analysis |
|
1 |
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 newick tree with HyPhy |
|
6 |
Annotate |
opens an IFrame to Apollo |
|
8 |
Annotate DESeq2/DEXSeq output tables |
Append annotation from GTF to differential expression tool outputs |
|
2 |
Annotate RNAz |
|
|
1 |
Annotate with DGI |
database info |
|
1 |
Annotate with DGI |
database info |
|
1 |
annotateMyIDs |
annotate a generic set of identifiers |
|
11 |
annotatePeaks |
|
|
4 |
Anosim |
Non-parametric multivariate analysis of changes in community structure |
|
5 |
Anova |
N-way anova. With ou Without interactions |
|
3 |
antaRNA |
Ant Colony Optimized RNA Sequence Design |
|
1 |
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 |
Apply elastic transformation |
with bUnwarpJ |
|
2 |
Apply raw transformation |
with bUnwarpJ |
|
2 |
Arithmetic Operations |
on tables |
|
2 |
Arriba |
detect gene fusions from STAR aligned RNA-Seq data |
|
4 |
Arriba Draw Fusions |
|
|
4 |
Arriba Get Filters |
to history |
|
4 |
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 |
ASHLAR |
Alignment by Simultaneous Harmonization of Layer/Adjacency Registration |
|
1 |
AssayGeneratorMetabo |
Assay library generation from DDA data (Metabolomics) |
|
3 |
Assemble with MIRA v3.4 |
Takes Sanger, Roche, Illumina, and Ion Torrent data |
|
2 |
Assign taxonomy |
to each sequence (assign_taxonomy) |
|
2 |
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 |
Automated multiple sequence |
alignment with pipelign |
|
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 |
b2bTools: Biophysical predictors for single sequences |
from their amino-acid sequences |
|
1 |
backtranseq |
Back translate a protein sequence |
|
7 |
Bakta |
genome annotation via alignment-free sequence identification |
|
2 |
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 Wiggle |
converts all types of RNA-seq data from .bam to .wig |
|
10 |
bam-to-bai |
converter |
|
1 |
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 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 |
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 |
Base Count |
|
|
1 |
Base Coverage |
of all intervals |
Quantification
|
5 |
BaselineFilter |
Removes the baseline from profile spectra using a top-hat filter. |
|
4 |
BaSiC Illumination |
ImageJ BaSiC shading correction for use with Ashlar |
|
1 |
basil |
Breakpoint detection, including large insertions |
|
1 |
Batch_correction |
Corrects intensities for signal drift and batch-effects |
|
4 |
bax2bam |
converts PacBio basecall format (bax.h5) into BAM |
Conversion
|
2 |
BayeScan |
Detecting natural selection from population-based genetic data |
|
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_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 csq |
Haplotype aware consequence predictor |
|
11 |
bcftools filter |
Apply fixed-threshold filters |
|
10 |
bcftools frameshifts |
plugin Annotate frameshift indels |
|
8 |
bcftools gtcheck |
Check sample identity |
|
10 |
bcftools isec |
Create intersections, unions and complements of VCF files |
|
11 |
bcftools merge |
Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file |
|
11 |
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 split-vep |
plugin Extracts fields from structured annotations such as INFO/CSQ |
|
4 |
bcftools stats |
Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats |
|
12 |
bcftools view |
VCF/BCF conversion, view, subset and filter VCF/BCF files |
|
14 |
bcftoolsView |
Convert, filter, subset VCF/BCF files |
|
1 |
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 |
Conversion
|
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 |
Between-table Correlation |
Correlation table between two tables and graphic representation |
|
2 |
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 |
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 |
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 |
BiSCoT |
Bionano scaffolding correction |
|
1 |
Bismark |
bisulfite mapper (bowtie) |
|
2 |
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 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 tabular |
Convert BLAST XML output to tabular |
Conversion
|
18 |
Blast2GO |
Maps BLAST results to GO annotation terms |
|
3 |
BlastXML to gapped GFF3 |
|
|
1 |
BlobToolKit |
genome assembly QC |
|
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 |
Bowtie2 |
- map reads against reference genome |
|
21 |
Boxplot |
of quality statistics |
|
2 |
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 UPGMA tree |
comparing samples (upgma_cluster) |
|
2 |
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 |
|
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 |
BWA-MEM2 |
- map medium and long reads (> 100 bp) against reference genome |
|
1 |
bwameth |
Fast and accurate aligner of BS-Seq reads. |
|
6 |
bwtool-lift |
Project data base-by-base into a new assembly using a liftOver chain file from UCSC |
|
1 |
Cactus |
whole-genome multiple sequence alignment |
|
7 |
Cactus: export |
whole-genome multiple sequence alignment to other formats |
|
9 |
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 alpha diversity |
on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity) |
|
2 |
Calculate beta diversity |
(pairwise sample dissimilarity) on one or many otu tables (beta_diversity) |
|
2 |
Calculate community metrics |
calculate community metrics from abundance data |
|
3 |
Calculate contig depths |
for MetaBAT2 |
|
3 |
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 |
Call and phase |
heterozygous SNPs |
|
4 |
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 |
cap3 |
Sequence Assembly tool |
DNA mapping
Mapping
Mapping assembly
Sequence assembly
|
2 |
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 collapsing hierarchical data to a specified functional level |
|
2 |
Categorize Elements |
satisfying criteria |
|
1 |
CCAT |
Control-based ChIP-seq Analysis Tool |
|
2 |
cd-hit |
Cluster or compare biological sequence datasets |
|
2 |
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 |
Cell types - build cell ontology map |
Create a mapping from labels to CL terms |
|
3 |
Cell types - combine tools outputs |
Combine predictions for single tool from multiple datasets |
|
4 |
Cell types - get consensus outputs |
across multiple tools |
|
4 |
Cell types - get empirical distribution |
for tool performance table |
|
3 |
Cell types - get tool p-values |
Get p-values for tool performance metrics |
|
3 |
Cell types - get tool performance table |
Get performance table for a list of outputs generated by various tools |
|
3 |
CellProfiler |
run a CellProfiler pipeline |
|
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 metadata value. |
|
6 |
chaos |
Create a chaos game representation plot for a sequence |
|
5 |
charge |
Protein charge plot |
|
5 |
Check Format |
Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files |
|
2 |
Check user's metadata mapping file |
for required data, valid format (validate_mapping_file) |
|
2 |
CheckM analyze |
Identify marker genes in bins and calculate genome statistics |
|
1 |
CheckM lineage_set |
Infer lineage-specific marker sets for each bin |
|
1 |
CheckM lineage_wf |
Assessing the completeness and contamination of genome bins using lineage-specific marker sets |
|
1 |
CheckM plot |
for assessing the quality of genome bins |
|
1 |
CheckM qa |
Assess bins for contamination and completeness |
|
1 |
CheckM taxon_set |
Generate taxonomic-specific marker set |
|
1 |
CheckM taxonomy_wf |
Analyze all genome bins with the same marker set |
|
1 |
CheckM tetra |
Calculate tetranucleotide signature of sequences |
|
1 |
CheckM tree |
Place bins in the genome tree |
|
1 |
CheckM tree_qa |
Assess phylogenetic markers in the genome tree |
|
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 |
cif2cell |
convert .cif file to .cell |
|
2 |
CIRCexplorer |
|
|
2 |
CIRCexplorer2 |
circular RNA analysis |
|
1 |
Circos |
visualizes data in a circular layout |
Visualisation
|
11 |
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 |
CITE-seq-Count |
Count CMO/HTO |
|
1 |
Clair3 |
germline small variant caller for long-reads |
|
2 |
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 |
Clip |
adapter sequences |
|
6 |
CLIP Peakcaller |
find CLIP peaks in blockbuster data |
|
1 |
Clipping Profile |
estimates clipping profile of RNA-seq reads from BAM or SAM file |
|
10 |
Close relatives |
: Discover familial relationships |
|
2 |
Closed-reference OTU picking |
Shotgun UniFrac workflow (pick_closed_reference_otus) |
|
2 |
ClustalW |
multiple sequence alignment program for DNA or proteins |
|
5 |
Cluster |
the intervals of a dataset |
Sequence clustering
Sequence merging
|
5 |
Cluster |
Assign sequences to OTUs (Operational Taxonomic Unit) |
|
4 |
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 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 |
Clustering using RaceID |
performs clustering, outlier detection, dimensional reduction |
|
6 |
ClusterMassTraces |
Creates pseudo spectra. |
|
2 |
ClusterMassTracesByPrecursor |
Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile. |
|
2 |
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-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 |
Codon count |
gives numbers of all different codons in the whole sequence |
|
1 |
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: pubmut |
render a JSON or YAML file to a pretty table |
|
1 |
Cojac: tabmut |
export cooccurrence mutations as a table |
|
1 |
Collapse |
sequences |
|
3 |
Collapse Collection |
into single dataset in order of the collection |
|
5 |
Collapse samples |
Collapse samples in a BIOM table and mapping file |
|
1 |
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 |
Color Deconvolution |
Color deconvolution |
|
2 |
ColorToGray |
converts color and channel-stacked images to grayscale |
|
2 |
Column arrange |
by header name |
|
2 |
Column Join |
on Collections |
|
5 |
Column Regex Find And Replace |
|
|
6 |
Combine FASTA and QUAL |
into FASTQ |
Aggregation
|
5 |
Combine MetaPhlAn2 and HUMAnN2 outputs |
to relate genus/species abundances and gene families/pathways abundances |
|
3 |
CometAdapter |
Annotates MS/MS spectra using Comet. |
|
3 |
Compalignp |
Fractional identities between alignments |
|
2 |
Compare |
multiple VCF datasets |
|
1 |
Compare BIOM tables |
Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. |
|
3 |
Compare diversity indicators |
with remote sensing data |
|
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 |
Complement |
intervals of a dataset |
Sequence coordinate conversion
|
6 |
CompNovo |
Performs a de novo peptide identification using the CompNovo engine. |
|
4 |
CompNovoCID |
Performs a de novo peptide identification using the CompNovo engine. |
|
4 |
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 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 |
Compute |
on rows |
|
10 |
Compute a PCA raster |
from remote sensing data |
|
1 |
Compute beta diversity distance matrices and generate PCoA plots |
(beta_diversity_through_plots) |
|
2 |
Compute biodiversity indices |
from remote sensing data |
|
1 |
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 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 physico-chemical properties |
for a set of molecules |
|
5 |
Compute quality statistics |
for SOLiD data |
|
1 |
Compute quality statistics |
|
|
3 |
Compute sequence length |
|
|
6 |
Compute spectral indices |
as NDVI from remote sensing data |
|
1 |
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 |
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 |
|
4 |
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 |
Conformer calculation |
for molecules (confab) with OpenBabel |
|
3 |
Consensus.seqs |
Find a consensus sequence for each OTU or phylotype |
|
6 |
ConsensusID |
Computes a consensus of peptide identifications of several identification engines. |
|
6 |
ConsensusMapNormalizer |
Normalizes maps of one consensusXML file |
|
5 |
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 |
Convert |
delimiters to TAB |
|
1 |
Convert |
SOLiD output to fastq |
|
1 |
Convert |
sequences to graphs |
|
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 ScIdx |
|
|
2 |
Convert BED to Feature Location Index |
|
|
1 |
Convert BED to GFF |
|
|
2 |
Convert binary image to EDM |
(Euclidean Distance Map) |
|
2 |
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 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 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 OBO to OWL |
|
|
1 |
Convert OBO to RDF |
|
|
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 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 |
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 genome bins in fasta format |
to scaffolds-to-bin table |
|
3 |
Converts GTF to Annotations file for Homer |
|
|
1 |
CoNvex |
Gap-cost alignMents for Long Reads |
|
2 |
Cooccurrence |
tests whether presence-absence patterns differ from chance |
|
6 |
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 |
coronaSPAdes |
SARS-CoV-2 de novo genome assembler |
|
6 |
Corr.axes |
correlation of data to axes |
|
5 |
correctGCBias |
uses the output from computeGCBias to generate GC-corrected BAM/CRAM files |
|
16 |
Correlation |
for numeric columns |
|
1 |
Cosine Content |
- measure the cosine content of the PCA projection |
|
4 |
Count |
occurrences of each record |
|
2 |
Count Covariates |
on BAM files |
|
1 |
Count GFF Features |
|
|
2 |
Count Objects |
in labled images |
|
1 |
Count sequences |
Count the sequences in a fasta file |
|
2 |
Count the sequences |
in a fasta file (count_seqs) |
|
2 |
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 |
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 |
CPAT |
coding potential assessment |
|
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 binary barcodes |
from regular barcodes. |
|
3 |
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 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 nested list |
based on filenames and batch sizes |
|
2 |
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 three-dimensional PCoA plots |
to be visualized with Emperor (make_emperor) |
|
2 |
Create.database |
creates a database file from a list, repnames, repfasta and contaxonomy file |
|
5 |
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 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 |
CruxAdapter |
Identifies MS/MS spectra using Crux. |
|
2 |
CryptoGenotyper |
classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data. |
|
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 |
cURL |
send cURL POST requests |
|
1 |
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 |
cuteSV |
detects long-read-based SVs |
|
1 |
cutseq |
Removes a specified section from a sequence |
|
5 |
CVInspector |
A tool for visualization and validation of PSI mapping and CV files. |
|
6 |
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 |
dan |
Calculates DNA RNA/DNA melting temperature |
|
5 |
DAS Tool |
for genome resolved metagenomics |
|
3 |
Data Fetch |
|
Query and retrieval
|
1 |
DatabaseFilter |
Filters a protein database (FASTA format) based on identified proteins |
|
5 |
Datamash |
(operations on tabular data) |
|
5 |
DAVID |
functional annotation for a list of genes |
|
1 |
DBKit Create |
database |
|
1 |
DBKit Extract |
entries |
|
1 |
DBKit Merge |
two databases |
|
1 |
dbnsfp.tabular-to-snpsiftdbnsfp |
converter |
|
3 |
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 |
Decharger |
Decharges and merges different feature charge variants of the same peptide. |
|
5 |
decontaminator |
Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies |
|
1 |
DecoyDatabase |
Create decoy sequence database from forward sequence database. |
|
5 |
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 |
Deletion Profile |
calculates the distributions of deleted nucleotides across reads |
|
6 |
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 |
DeMeanderize |
Orders the spectra of MALDI spotting plates correctly. |
|
4 |
Describe samples |
and replicates |
|
11 |
Descriptors |
calculated with RDKit |
|
4 |
descseq |
Alter the name or description of a sequence |
|
5 |
DESeq2 |
Determines differentially expressed features from count tables |
Differential gene expression profiling
RNA-Seq quantification
|
22 |
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 |
DEWSeq |
- A sliding window based peak caller for eCLIP/iCLIP data |
|
1 |
DEXSeq |
Determines differential exon usage from count tables |
|
10 |
DEXSeq-Count |
Prepare and count exon abundancies from RNA-seq data |
|
10 |
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 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 |
Differential Cleavage |
: Select SNPs differentially cut by specified restriction enzymes |
|
2 |
Differential expression analysis |
using a Trinity assembly |
|
11 |
diffseq |
Find differences between nearly identical sequences |
|
5 |
digest |
Protein proteolytic enzyme or reagent cleavage digest |
|
5 |
Digestor |
Digests a protein database in-silico. |
|
4 |
DigestorMotif |
digests a protein database in-silico |
|
4 |
Dihedral Analysis |
Time series of dihedrals |
|
5 |
DISCO |
to assemble metagenomics data using an overlap-layout-consensus (OLC) approach |
|
2 |
Discriminant Analysis |
|
|
12 |
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 |
DNAdiff |
Evaluate similarities/differences between two sequences |
Read mapping
Sequence alignment
|
5 |
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 and Extract Reads in BAM |
format from NCBI SRA |
Data retrieval
Formatting
|
24 |
Download and Generate Pileup Format |
from NCBI SRA |
|
9 |
Download run data |
from EBI Metagenomics database |
|
1 |
downloads |
via lftps |
|
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 |
DRAM annotate |
metagenome-assembled-genomes (MAGs) |
|
1 |
DRAM distill |
metagenome-assembled-genomes (MAGs) |
|
1 |
DRAM find neighborhoods |
around genes of interest |
|
1 |
DRAM merge multiple annotations |
into a single set |
|
1 |
DRAM strain annotations |
down to genes of interest |
|
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 |
DREME |
- Discriminative Regular Expression Motif Elicitation |
|
4 |
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 |
DTAExtractor |
Extracts spectra of an MS run file to several files in DTA format. |
|
5 |
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 |
Perform differential expression of count data |
Differential gene expression profiling
RNA-seq read count analysis
|
10 |
edta |
Whole-genome de-novo TE annotation |
|
1 |
EGA Download Client |
|
|
5 |
eggNOG Mapper |
functional sequence annotation by orthology |
|
10 |
EGSEA |
easy and efficient ensemble gene set testing |
|
4 |
EICExtractor |
Extracts intensities from dedicates positions in a LC/MS map |
|
5 |
einverted |
Finds DNA inverted repeats |
|
5 |
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 |
Enhance contrast |
|
|
2 |
EnhanceOrSuppressFeatures |
to improve subsequent identification of objects |
|
2 |
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 |
epestfind |
Finds PEST motifs as potential proteolytic cleavage sites |
|
5 |
EpiCSeg - Chromatin segmentation |
|
|
1 |
Epifany |
Runs a Bayesian protein inference. |
|
2 |
equicktandem |
Finds tandem repeats |
|
5 |
ERPairFinder |
Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. |
|
4 |
est2genome |
Align EST and genomic DNA sequences |
|
5 |
Estimate Abundance at Taxonomic Level |
Bayesian Reestimation of Abundance with KrakEN |
Statistical calculation
|
3 |
Estimate Library Complexity |
|
|
3 |
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 |
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 |
Evaluation of RRIs using CheRRI |
|
|
1 |
ExomeDepth |
Calls copy number variants (CNVs) from targeted sequence data |
|
1 |
Exonerate |
pairwise sequence comparison |
|
4 |
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 |
ExternalCalibration |
Applies an external mass recalibration. |
|
6 |
Extract alignment ends |
from SAM or BAM |
|
3 |
Extract and cluster differentially expressed transcripts |
from a Trinity assembly |
|
12 |
Extract barcodes |
according to pattern |
|
3 |
Extract clusters of MD trajectories |
from linkage matrix data |
|
3 |
Extract CuffDiff |
tabular files from a cummeRbund database |
|
2 |
Extract element identifiers |
of a list collection |
|
2 |
Extract energy components with GROMACS |
|
|
7 |
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 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 sequences from GenBank |
files (CDS, gene ...) |
|
1 |
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 |
FalseDiscoveryRate |
Estimates the false discovery rate on peptide and protein level using decoy searches. |
|
7 |
fargene |
Fragmented antibiotic resistance gene identifier |
|
2 |
faSplit |
Split a FASTA file |
|
3 |
FASTA header converter |
to append species information |
|
1 |
FASTA Merge Files and Filter Unique Sequences |
Concatenate FASTA database files together |
|
4 |
Fasta nucleotide color plot |
|
|
2 |
Fasta nucleotide color plot |
|
|
1 |
Fasta regular expression finder |
Search in fasta for regexp match |
|
1 |
Fasta Statistics |
Display summary statistics for a fasta file. |
|
5 |
FASTA Width |
formatter |
|
3 |
fasta-to-fai |
converter |
|
1 |
FASTA-to-Tabular |
converter |
|
3 |
fasta_to_gspan |
|
|
3 |
FastaCLI |
Appends decoy sequences to FASTA files |
|
6 |
FastANI |
fast alignment-free computation of whole-genome Average Nucleotide Identity |
|
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 |
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 splitter |
on joined paired end reads |
Splitting
|
6 |
FASTQ Summary Statistics |
by column |
Sequence assembly validation
|
4 |
FASTQ to FASTA |
converter |
Conversion
|
5 |
FASTQ to FASTA |
converter from FASTX-toolkit |
Sequence conversion
|
6 |
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 |
FastQC |
Read Quality reports |
Sequence composition calculation
Sequencing quality control
Statistical calculation
|
18 |
FASTQE |
visualize fastq files with emoji's 🧬😎 |
|
5 |
fastqillumina-to-fqtoc |
converter |
|
1 |
FastqToSam |
convert Fastq data into unaligned BAM |
|
19 |
FASTTREE |
build maximum-likelihood phylogenetic trees |
Phylogenetic analysis
Phylogenetic inference (from molecular sequences)
|
4 |
faToVcf |
Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs |
|
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 |
FeatureFinderCentroided |
Detects two-dimensional features in LC-MS data. |
|
5 |
FeatureFinderIdentification |
Detects features in MS1 data based on peptide identifications. |
|
5 |
FeatureFinderIsotopeWavelet |
Detects two-dimensional features in LC-MS data. |
|
5 |
FeatureFinderMetabo |
Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. |
|
5 |
FeatureFinderMetaboIdent |
Detects features in MS1 data based on metabolite identifications. |
|
2 |
FeatureFinderMRM |
Detects two-dimensional features in LC-MS data. |
|
4 |
FeatureFinderMultiplex |
Determination of peak ratios in LC-MS data |
|
7 |
FeatureFinderSuperHirn |
Finds mass spectrometric features in mass spectra. |
|
5 |
FeatureLinkerLabeled |
Groups corresponding isotope-labeled features in a feature map. |
|
5 |
FeatureLinkerUnlabeled |
Groups corresponding features from multiple maps. |
|
5 |
FeatureLinkerUnlabeledKD |
Groups corresponding features from multiple maps. |
|
4 |
FeatureLinkerUnlabeledQT |
Groups corresponding features from multiple maps. |
|
4 |
FEELnc |
FlExible Extraction of LncRNA |
|
6 |
Fetch closest non-overlapping feature |
for every interval |
Filtering
|
4 |
Fetch Indels |
from 3-way alignments |
|
1 |
Fetch taxonomic representation |
|
|
2 |
FFEval |
Evaluation tool for feature detection algorithms. |
|
4 |
fgsea |
- fast preranked gene set enrichment analysis |
|
3 |
FidoAdapter |
Runs the protein inference engine Fido. |
|
6 |
FileConverter |
Converts between different MS file formats. |
|
5 |
FileFilter |
Extracts or manipulates portions of data from peak, feature or consensus-feature files. |
|
5 |
FileInfo |
Shows basic information about the file, such as data ranges and file type. |
|
5 |
FileMerger |
Merges several MS files into one file. |
|
5 |
Filter |
data on any column using simple expressions |
Formatting
|
2 |
Filter |
with scanpy |
|
7 |
Filter |
a set of molecules from a file |
|
6 |
Filter |
a VCF file |
|
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 Combined Transcripts |
using tracking file |
|
1 |
Filter FASTA |
on the headers and/or the sequences |
|
5 |
Filter fasta |
to remove sequences based on input criteria (filter_fasta) |
|
2 |
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 Species |
|
1 |
Filter MAF blocks |
by Size |
|
1 |
Filter OTUs from an OTU table |
based on their observation counts or identifier (filter_otus_from_otu_table) |
|
2 |
Filter pileup |
on coverage and SNPs |
|
3 |
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 sequence alignment |
by removing highly variable regions (filter_alignment) |
|
2 |
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 species |
with rare and low abundances |
|
2 |
Filter Tabular |
|
|
5 |
Filter taxa from an OTU table |
(filter_taxa_from_otu_table) |
|
2 |
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 |
Filters samples from an OTU table |
on the basis of the number of observations in that sample, or on the basis of sample metadata (filter_samples_from_otu_table) |
|
2 |
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 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-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 |
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 |
FlashLFQ |
ultrafast label-free quantification for mass-spectrometry proteomics |
|
5 |
Flight curve |
compute the regional expected pattern of abundance |
|
1 |
Flye |
de novo assembler for single molecule sequencing reads |
Genome assembly
|
8 |
footprint |
|
|
1 |
Format |
tree and trait tables |
|
2 |
Format cd-hit outputs |
to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file |
|
2 |
Format Fastq sequences and barcode data |
(extract_barcodes) |
|
2 |
Format MetaPhlAn2 |
output to extract abundance at different taxonomic levels |
|
2 |
Format MetaPhlAn2 |
output for Krona |
|
2 |
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 |
Fragmenter |
splits a molecule in fragments |
|
1 |
freak |
Residue/base frequency table or plot |
|
5 |
FreeBayes |
bayesian genetic variant detector |
|
12 |
Freyja: Aggregate and visualize |
demixed results |
|
1 |
Freyja: Bootstrapping |
method |
|
1 |
Freyja: Call variants |
and get sequencing depth information |
|
1 |
Freyja: Demix |
lineage abundances |
|
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 |
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 |
FuzzyDiff |
Compares two files, tolerating numeric differences. |
|
4 |
g:Profiler |
tools for functional profiling of gene lists |
|
1 |
Garnett - check markers |
Check marker file to filter out markers of suboptimal quality |
|
1 |
Garnett - classify cells |
Classify cells into cell types |
|
1 |
Garnett - get feature genes |
Obtain a list of genes used as features in classification model |
|
1 |
Garnett - get standard output |
Get final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package |
|
1 |
Garnett - train classifier |
Train classifier based on marker gene list |
|
1 |
Garnett - transform markes |
Transform marker files from Single Cell Expression Atlas format to that compatible with Garnett |
|
1 |
Garnett - update markers |
Update marker file by filtering out suboptimal markers |
|
1 |
garnier |
Predicts protein secondary structure |
|
5 |
Gate Finder |
displays a series of gating outcomes using Vitessce |
|
1 |
GATK4 Mutect2 |
- Call somatic SNVs and indels via local assembly of haplotypes |
|
8 |
GC Skew |
calculates skew over genomic sequences |
Nucleic acid property calculation
|
10 |
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 burden |
perform sample-wise gene-level burden calculations |
|
4 |
GEMINI database info |
Retrieve information about tables, columns and annotation data stored in a GEMINI database |
|
4 |
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 pathways |
Map genes and variants to KEGG pathways |
|
5 |
GEMINI qc |
Quality control tool |
|
5 |
GEMINI query |
Querying the GEMINI database |
|
5 |
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 and EBML |
to GFF converter |
|
1 |
Genbank to GFF3 |
converter |
|
2 |
genbank-to-genbank.gz |
converter |
|
1 |
genbank.gz-to-genbank |
converter |
|
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 |
Generalized linear models |
for classification and regression |
|
11 |
Generate |
random samples with controlled size and complexity |
|
12 |
Generate A Matrix |
for using PC and LDA |
|
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 pileup |
from BAM dataset |
|
3 |
Generate SuperTranscripts |
from a Trinity assembly |
|
6 |
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 |
genform |
Generation of molecular formulas by high-resolution MS and MS/MS data |
|
1 |
Genome annotation statistics |
|
|
1 |
GenomeScope |
reference-free genome profiling |
|
3 |
GenomicSuperSignature |
interpretation of RNAseq experiments |
|
1 |
Genrich |
Detecting sites of genomic enrichment |
|
3 |
Get all term synonyms |
of a given OBO term |
|
1 |
Get all terms |
of a given OBO term |
|
1 |
Get all the relationship IDs and definitions |
from the given OBO ontology |
|
2 |
Get all the relationship IDs and names |
from the given OBO ontology |
|
2 |
Get all the relationship IDs and namespaces |
from the given OBO ontology |
|
1 |
Get all the relationship types |
from the given OBO ontology |
|
2 |
Get all the term IDs and term names |
of a given OBO ontology |
|
1 |
Get child terms |
of a given OBO term |
|
1 |
Get crosslinked nucleotides |
from full alignments |
|
3 |
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 organelle from reads |
|
|
1 |
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 PubMed abstracts |
by PMID IDs |
|
1 |
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 sequences by Ensembl ID |
using REST API |
|
3 |
Get species occurrences data |
from GBIF, ALA, iNAT and others |
|
1 |
Get subontology |
from a given OBO term |
|
1 |
Get the ancestor terms of a given OBO term |
Collects the ancestor terms from a given term in the given OBO ontology |
|
2 |
Get the descendent terms |
of a given OBO term |
|
1 |
Get the parent terms |
of a given OBO term |
|
1 |
Get the root terms |
of a given OBO term |
|
1 |
Get the terms |
filtered by a relationship type |
|
1 |
Get the terms that are related |
by a concrete relationship type |
|
2 |
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 |
GetFastaBed |
use intervals to extract sequences from a FASTA file |
|
20 |
getorf |
Finds and extracts open reading frames (ORFs) |
|
5 |
GFA to FASTA |
Convert Graphical Fragment Assembly files to FASTA format |
|
4 |
gfastats |
the swiss army knife for genome assembly |
|
8 |
GFF converter |
to GenBank or embl |
|
1 |
GFF-to-BED |
converter |
Conversion
|
1 |
GFF3 to Apollo Annotations |
|
|
8 |
gff3.bz2-to-gff3 |
converter |
|
1 |
GffCompare |
compare assembled transcripts to a reference annotation |
|
5 |
gffread |
Filters and/or converts GFF3/GTF2 records |
|
7 |
GLASSgo |
sRNA homolog finder |
|
2 |
Glimmer ICM builder |
|
|
1 |
Glimmer3 |
Predict ORFs in prokaryotic genomes (knowlegde-based) |
|
1 |
Glimmer3 |
Predict ORFs in prokaryotic genomes (not knowlegde-based) |
|
1 |
GMAJ |
Multiple Alignment Viewer |
|
1 |
GNPSExport |
Tool to export consensus features into MGF format |
|
2 |
GOEnrichment |
performs GO enrichment analysis of a set of gene products |
|
2 |
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 |
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 check |
to provide information about GROMACS input files |
|
2 |
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 RMSD calculation |
of molecular structures |
|
1 |
GROMACS RMSF calculation |
of molecular structures |
|
1 |
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-interval_index |
converter |
|
1 |
GTF2GeneList |
extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer |
|
6 |
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 |
Hapo-G |
genome polishing |
|
1 |
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 |
HE/ MALDI Image Registration |
Registration of MALDI and HE Image |
|
1 |
Heatmap |
Heatmap of the dataMatrix |
|
2 |
Heatmap w ggplot |
|
|
6 |
Heatmap.bin |
Generate a heatmap for OTUs |
|
5 |
Heatmap.sim |
Generate a heatmap for pariwise similarity |
|
5 |
heatmap2 |
|
|
6 |
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 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 |
Hifiasm_meta |
for metagenome assembly using Hifi reads |
|
2 |
hifive |
manipulate, analyze, and plot HiC and 5C chromatin interaction data |
|
2 |
HighResPrecursorMassCorrector |
Corrects the precursor mass and charge determined by the instrument software. |
|
5 |
HISAT2 |
A fast and sensitive alignment program |
|
19 |
Histogram |
of a numeric column |
|
4 |
Histogram equalization |
automatic histogram equalization |
|
1 |
Histogram w ggplot2 |
|
|
7 |
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 |
htseq-clip |
- A toolset for the analysis of eCLIP/iCLIP datasets |
|
1 |
htseq-count |
- Count aligned reads in a BAM file that overlap features in a GFF file |
|
9 |
Human Cell Atlas Matrix Downloader |
retrieves expression matrices and metadata from the Human Cell Atlas. |
|
3 |
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 |
HyPo |
super fast and accurate polisher for long read genome assemblies |
|
1 |
ID choice |
Choosing a particular column in your metadata to be considered as Identifiers |
|
2 |
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 |
IDConflictResolver |
Resolves ambiguous annotations of features with peptide identifications |
|
5 |
idconvert |
Convert mass spectrometry identification files |
|
4 |
IDDecoyProbability |
Estimates peptide probabilities using a decoy search strategy.WARNING: This util is deprecated. |
|
3 |
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 |
IDExtractor |
Extracts 'n' peptides randomly or best 'n' from idXML files. |
|
3 |
IDFileConverter |
Converts identification engine file formats. |
|
6 |
IDFilter |
Filters results from protein or peptide identification engines based on different criteria. |
|
6 |
IDMapper |
Assigns protein/peptide identifications to features or consensus features. |
|
5 |
IDMassAccuracy |
Calculates a distribution of the mass error from given mass spectra and IDs. |
|
5 |
IDMerger |
Merges several protein/peptide identification files into one file. |
|
6 |
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 |
IDPosteriorErrorProbability |
Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. |
|
5 |
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 |
IDRipper |
Split protein/peptide identification file into several files according to annotated file origin. |
|
4 |
IDRTCalibration |
Can be used to calibrate RTs of peptide hits linearly to standards. |
|
4 |
IDScoreSwitcher |
Switches between different scores of peptide or protein hits in identification data |
|
6 |
IDSplitter |
Splits protein/peptide identifications off of annotated data files |
|
4 |
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 Converter |
|
|
3 |
Image Info |
Show Image Info |
|
2 |
Image Montage |
|
|
3 |
Image Registration |
based on intensity information |
|
3 |
ImageMath |
perform simple mathematical operations on images |
|
2 |
Import Anndata and loom |
from different format |
|
9 |
Inbreeding and kinship |
: Analyze the pedigree without genomic data |
|
2 |
inchi-to-mol |
converter |
|
2 |
InclusionExclusionListCreator |
Creates inclusion and/or exclusion lists. |
|
2 |
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 |
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 |
InspectAdapter |
Annotates MS/MS spectra using Inspect. |
|
3 |
instaGRAAL |
Large genome reassembly based on Hi-C data |
|
2 |
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 |
IntaRNA |
Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. |
|
4 |
Integron Finder |
is a program that detects integrons in DNA sequences |
Genome annotation
Nucleic acid sequence feature detection
Protein sequence feature detection
Sequence motif recognition
|
2 |
Intensity Check |
Statistical measures, number of missing values and mean fold change |
|
2 |
InternalCalibration |
Applies an internal mass recalibration. |
|
5 |
InterProphet |
Combine Peptide Prophet results from multiple search engines |
|
2 |
InterProScan |
functional annotation |
|
9 |
Intersect |
multiple VCF datasets |
|
2 |
Intersect |
the intervals of two datasets |
Filtering
|
6 |
Intersect intervals |
find overlapping intervals in various ways |
|
22 |
IQ-TREE |
Phylogenomic / evolutionary tree construction from multiple sequences |
|
7 |
Iris |
Refine insertion sequences |
|
3 |
ISEScan |
Insertion Sequence Elements detection in prokaryotic genomes |
|
1 |
IsobaricAnalyzer |
Calculates isobaric quantitative values for peptides |
|
4 |
isochore |
Plots isochores in large DNA sequences |
|
5 |
IsoformSwitchAnalyzeR |
statistical identification of isoform switching |
|
1 |
Isoplot: Generate plots from isocor output |
|
|
2 |
Iterative Mapping |
iteratively maps the raw reads of RNA structural data to the reference transcriptome |
|
1 |
ITSx |
identifies ITS sequences and extracts the ITS region |
|
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 |
IVR |
indicator |
|
1 |
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 |
JAMM |
Calls peaks on NGS data |
|
1 |
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 |
two files |
|
12 |
Join |
HUMAnN2 generated tables |
|
4 |
Join |
the intervals of two datasets side-by-side |
Aggregation
|
5 |
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 |
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 |
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 |
Kinfold |
Simulates the stochastic folding kinetics of RNA sequences into secondary structures. |
|
1 |
KING |
Kinship-based INference for GWAS |
|
2 |
Kinwalker |
cotranscriptional folding of RNAs |
|
1 |
Kleborate |
screen genome assemblies of Klebsiella pneumoniae |
|
1 |
KOBAS Annotate |
KEGG Orthology Based Annotation System |
|
3 |
KOBAS Identify |
KEGG Orthology Based Annotation System |
|
3 |
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-biom |
Create BIOM-format tables from kraken output |
|
2 |
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 |
Krakentools: Calculates alpha diversity |
from the Bracken abundance estimation file |
|
1 |
Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) |
from Kraken, Krona and Bracken files |
|
1 |
Krakentools: Convert kraken report file |
to krona text file |
|
1 |
Krona pie chart |
from taxonomic profile |
|
10 |
Kronik |
processes Hardklor features to find peptides by chromatographic profiling |
|
4 |
Label free protein |
summarisation and quantitation |
|
1 |
Label to Points |
Converts label image to points |
|
2 |
LabeledEval |
Evaluation tool for isotope-labeled quantitation experiments. |
|
4 |
LAJ |
Pairwise Alignment Viewer |
|
1 |
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 |
Libshuff |
Cramer-von Mises tests communities for the same structure |
|
5 |
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 |
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 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 |
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 |
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 |
LowMemPeakPickerHiRes |
Finds mass spectrometric peaks in profile mass spectra. |
|
4 |
LowMemPeakPickerHiResRandomAccess |
Finds mass spectrometric peaks in profile mass spectra. |
|
2 |
LowMemPeakPickerHiResRandomAccess |
Finds mass spectrometric peaks in profile mass spectra. |
|
1 |
LPS |
LASSO-Patternsearch algorithm |
|
1 |
LuciphorAdapter |
Modification site localisation using LuciPHOr2. |
|
5 |
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 |
MaAsLin 2 |
Microbiome Multivariable Association with Linear Models |
|
1 |
Machine Learning Visualization Extension |
includes several types of plotting for machine learning |
|
6 |
MACS |
Model-based Analysis of ChIP-Seq |
|
4 |
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 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 |
MAGeCK count |
- collect sgRNA read counts from read mapping files |
|
8 |
MAGeCK GSEA |
- a fast implementation of Gene Set Enrichment Analysis |
|
4 |
MAGeCK mle |
- perform maximum-likelihood estimation of gene essentiality scores |
|
5 |
MAGeCK pathway |
- given a ranked gene list, test whether one pathway is enriched |
|
4 |
MAGeCKs test |
- given a table of read counts, perform the sgRNA and gene ranking |
|
5 |
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 OTU table |
Make an OTU table from an OTU map and a taxonomy assignment file |
|
1 |
Make phylogeny |
(make_phylogeny) |
|
2 |
Make strain profiles |
|
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Make strain profiles |
|
|
3 |
Make taxonomy summary charts |
based on taxonomy assignment (plot_taxa_summary) |
|
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 |
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 |
Mantel |
Mantel correlation coefficient between two matrices. |
|
5 |
Map annotation ids |
on a Maker annotation |
|
5 |
Map diversity |
from remote sensing data |
|
1 |
Map peptides to a bed file |
for viewing in a genome browser |
|
3 |
map plot |
gridded (lat/lon) netCDF data |
|
2 |
Map with BFAST |
|
|
1 |
Map with Bowtie for Illumina |
|
|
7 |
Map with Bowtie for SOLiD |
|
|
1 |
Map with BWA |
- map short reads (< 100 bp) against reference genome |
|
12 |
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 |
MapAlignerIdentification |
Corrects retention time distortions between maps based on common peptide identifications. |
|
3 |
MapAlignerPoseClustering |
Corrects retention time distortions between maps using a pose clustering approach. |
|
4 |
MapAlignerSpectrum |
Corrects retention time distortions between maps by spectrum alignment. |
|
3 |
MapAlignerTreeGuided |
Tree guided correction of retention time distortions between maps. |
|
2 |
MapBed |
apply a function to a column for each overlapping interval |
|
21 |
MapNormalizer |
Normalizes peak intensities in an MS run. |
|
4 |
Mapper |
for long, error-prone reads, like Nanopore ONT and PacBio |
|
1 |
MapRTTransformer |
Applies retention time transformations to maps. |
|
5 |
MapStatistics |
Extract extended statistics on the features of a map for quality control. |
|
4 |
MaRaClusterAdapter |
Facilitate input to MaRaCluster and reintegrate. |
|
2 |
MarkDuplicates |
examine aligned records in BAM datasets to locate duplicate molecules |
|
17 |
MarkDuplicatesWithMateCigar |
examine aligned records in BAM datasets to locate duplicate molecules |
|
16 |
marscan |
Finds MAR/SAR sites in nucleic sequences |
|
5 |
MascotAdapter |
Annotates MS/MS spectra using Mascot. |
|
4 |
MascotAdapterOnline |
Annotates MS/MS spectra using Mascot. |
|
4 |
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 |
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 |
MassCalculator |
Calculates masses and mass-to-charge ratios of peptide sequences |
|
5 |
MassTraceExtractor |
Detects mass traces in centroided LC-MS data. |
|
3 |
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 |
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 |
MaxQuant Phosphopeptide ANOVA |
Runs ANOVA and KSEA for phosphopeptides. |
Dendrogram visualisation
Enrichment analysis
Heat map generation
Protein interaction network analysis
Standardisation and normalisation
Statistical inference
|
2 |
MaxQuant Phosphopeptide Preprocessing |
Prep phosphoproteomic MaxQuant output for statistical anlaysis. |
Aggregation
Conversion
Sequence annotation
Sequence database search
|
2 |
MCL |
The Markov Cluster Algorithm, a cluster algorithm for graphs |
Clustering
|
2 |
MCQUANT |
a module for single-cell data extraction |
|
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 |
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 |
Merge |
multiple VCF datasets |
|
2 |
Merge |
the overlapping intervals of a dataset |
Sequence merging
|
5 |
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 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 PCR duplicates |
according to UMIs |
|
3 |
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 |
merger |
Merge two overlapping nucleic acid sequences |
|
5 |
MergeSamFiles |
merges multiple SAM/BAM datasets into one |
|
14 |
Merging |
fragmented molecules |
|
1 |
Merqury |
evaluate the assembly quality |
Genome assembly
|
4 |
Meryl |
a genomic k-mer counter and sequence utility |
Genome assembly
|
8 |
Mesmer |
Mesmer for whole-cell segmentation of multiplexed tissue imaging data |
|
3 |
MetaBAT2 |
metagenome binning |
|
3 |
MetaboliteAdductDecharger |
Decharges and merges different feature charge variants of the same metabolite. |
|
3 |
MetaboliteSpectralMatcher |
Perform a spectral library search. |
|
4 |
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 |
Metagenome Contributions |
of OTUs to user-specified functions |
|
2 |
metagenomeSeq Normalization |
Cumulative sum scaling |
|
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 |
MetaPhlAn2 |
to profile the composition of microbial communities |
|
2 |
metaplasmidSPAdes |
extract and assembly plasmids from metagenomic data |
|
6 |
MetaProSIP |
Performs proteinSIP on peptide features for elemental flux analysis. |
|
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 |
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 |
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 |
Minfi DMP |
to find differentially methylated positions |
|
1 |
Minfi DMR |
to find differentially methylated regions |
|
1 |
Minfi Drop SNPs |
drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension |
|
1 |
Minfi Get Beta |
obtain Beta value matrix |
|
1 |
Minfi Get CN |
get the coordinating node associated with this D1Client object |
|
1 |
Minfi Get M |
returns the Fisher information corresponding to a model and a design |
|
1 |
Minfi Get SNPs |
retrieve the chromosome and the position of each SNP |
|
1 |
Minfi Map to Genome |
mapping Ilumina methylation array data to the genome |
|
1 |
Minfi Mset |
Create objects contains CpGs signals |
|
1 |
Minfi Preprocess Funnorm |
implements the functional normalization algorithm |
|
1 |
Minfi Preprocess Quantile |
implements stratified quantile normalization preprocessing |
|
1 |
Minfi QC |
provides a simple quality control matrix and plot |
|
1 |
Minfi Read 450k |
load .IDAT files |
|
1 |
Minfi Rset |
store Beta values and/or M values |
|
1 |
Minia |
Short-read assembler based on a de Bruijn graph |
|
3 |
miniasm |
Ultrafast de novo assembly for long noisy reads |
|
7 |
minipolish |
polishing miniasm assemblies |
|
1 |
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 |
miRNAture |
Computational detection of canonical microRNAs |
|
1 |
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 |
MITOS |
de-novo annotation of metazoan mitochondrial genomes |
|
2 |
MITOS2 |
de-novo annotation of metazoan mitochondrial genomes |
|
3 |
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 |
Model Prediction |
predicts on new data using a preffited model |
|
7 |
Model temporal trend |
with a simple linear regression |
|
1 |
Model Validation |
includes cross_validate, cross_val_predict, learning_curve, and more |
|
11 |
Modify/convert GROMACS trajectories |
using trjconv and trjcat |
|
8 |
moFF |
extracts MS1 intensities from spectrum files |
|
5 |
mol2-to-mol |
converter |
|
2 |
Molecule recognition |
in PDF documents (OSRA) |
|
1 |
Molecule to fingerprint |
conversion to several different fingerprint formats |
|
5 |
Monocle3 create |
a Monocle3 object from input data |
|
4 |
Monocle3 diffExp |
of genes along a trajectory |
|
4 |
Monocle3 learnGraph |
between cells in dimensionality reduced space |
|
3 |
Monocle3 orderCells |
along trajectories |
|
3 |
Monocle3 partition |
of cells into groups |
|
3 |
Monocle3 plotCells |
in the reduced dimensionality space |
|
5 |
Monocle3 preprocess |
a Monocle3 object to an initially dimensionally reduced space |
|
3 |
Monocle3 reduceDim |
for downstream analysis |
|
3 |
Monocle3 top markers |
for cell groups |
|
1 |
Morpheus |
database search algorithm for high-resolution tandem mass spectra |
|
2 |
mothur.ref.taxonomy-to-mothur.seq.taxonomy |
converter |
|
2 |
Motif_Finder_Plot |
|
|
2 |
mQC |
quality control of ribosome profiling mapping results |
|
2 |
MRMMapper |
MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) |
|
4 |
MRMPairFinder |
Util which can be used to evaluate labeled pair ratios on MRM features. |
|
5 |
MRMTransitionGroupPicker |
Picks peaks in SRM/MRM chromatograms. |
|
5 |
MS-GF+ |
Identifies peptides in tandem mass spectra using the MS-GF+ search engine. |
|
5 |
MSABOOT |
Output PHYLIP file with bootstrapped multiple sequence alignment data |
|
3 |
msbar |
Mutate sequence beyond all recognition |
|
5 |
msconvert |
Convert and/or filter mass spectrometry files |
|
5 |
msconvert Subset Peak List |
against list of scan numbers or indices. |
|
1 |
MSFraggerAdapter |
Peptide Identification with MSFragger.Important note:The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available for use on related service offerings supported by the University of Tubingen and the Center forIntegrative Bioinformatics. Per the license agreement the use of the pipeline and associated materials is for academic research, non-commercial or educational purposes. Any commercial use inquiries must be directed to the University of Michigan Technology Transfer Office at techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the University of Michigan.For details, please see the supplied license file or https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt |
|
4 |
MSGFPlusAdapter |
MS/MS database search using MS-GF+. |
|
6 |
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 |
MSSimulator |
A highly configurable simulator for mass spectrometry experiments. |
|
4 |
MSstats |
statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry |
|
5 |
MSstatsConverter |
Converter to input for MSstats |
|
2 |
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 |
Multilevel |
Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package |
|
1 |
MultiplexResolver |
Completes peptide multiplets and resolves conflicts within them. |
|
4 |
MultiQC |
aggregate results from bioinformatics analyses into a single report |
Statistical calculation
Validation
Visualisation
|
18 |
Multivariate |
PCA, PLS and OPLS |
|
2 |
Mummer |
Align two or more sequences |
Read mapping
Sequence alignment
|
5 |
MUMmer dotplot |
Combine mummer/nucmer/promer with mummerplot |
|
4 |
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 |
MuSpinSim Configure |
define simulation parameters |
|
2 |
MuSpinSim Plot |
plot values generated from MuSpinSim |
|
2 |
MuSpinSim Simulate |
perform spin dynamics calculations for muon science experiments |
|
2 |
Mutate Codons |
with SNPs |
|
1 |
MyriMatch |
Identify peptides in tandem mass spectra. |
|
4 |
MyriMatchAdapter |
Annotates MS/MS spectra using MyriMatch. |
|
2 |
mz to sqlite |
Extract mzIdentML and associated proteomics datasets into a SQLite DB |
|
5 |
MzMLSplitter |
Splits an mzML file into multiple parts |
|
4 |
MzTabExporter |
Exports various XML formats to an mzTab file. |
|
5 |
Naive Variant Caller (NVC) |
- tabulate variable sites from BAM datasets |
|
5 |
NanoComporeDB |
Process SampComp results database |
|
3 |
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+ blastp |
Search protein database with protein query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
19 |
NCBI BLAST+ blastx |
Search protein database with translated nucleotide query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
18 |
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+ tblastx |
Search translated nucleotide database with translated nucleotide query sequence(s) |
Data retrieval
Database search
Sequence similarity search
|
19 |
NCBI Datasets Gene |
download gene sequences and metadata |
|
2 |
NCBI Datasets Genomes |
download genome sequence, annotation and metadata |
|
12 |
NCBI ECitMatch |
search NCBI for citations in PubMed |
|
5 |
NCBI EFetch |
fetch records from NCBI |
|
5 |
NCBI EGQuery |
Provides the number of records retrieved in all Entrez databases by a single text query. |
|
5 |
NCBI EInfo |
fetch NCBI database metadata |
|
5 |
NCBI ELink |
link UIDs from one database to another |
|
5 |
NCBI EPost |
post UIDs to NCBI History Server |
|
5 |
NCBI ESearch |
search NCBI Databases by text query |
|
5 |
NCBI ESummary |
fetch summary of history/ids |
|
5 |
NCBI get species taxids |
|
|
2 |
Nearest Neighbors Classification |
|
|
2 |
Nearest Neighbors Classification |
|
|
11 |
necat |
Error correction and de-novo assembly for ONT Nanopore reads |
|
1 |
needle |
Needleman-Wunsch global alignment |
|
5 |
neostore.zip-to-neostore |
converter |
|
1 |
netboxr |
enables automated discovery of biological process modules by network analysis. |
|
1 |
NetCDF timeseries Extractor |
Extract and plot time series |
|
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 |
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 |
NextDenovo |
string graph-based de novo assembler for long reads |
|
1 |
NGSfilter |
Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers |
|
3 |
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 |
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_Normalization |
Normalization of NMR bucketed and integrated spectra |
|
1 |
NMR_Preprocessing |
Preprocessing of 1D NMR spectra |
|
4 |
NMR_Read |
Read Bruker NMR raw files |
|
3 |
NoiseFilterGaussian |
Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). |
|
4 |
NoiseFilterSGolay |
Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. |
|
5 |
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.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 |
NovorAdapter |
Template for Tool creation |
|
3 |
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 |
NucleicAcidSearchEngine |
Annotate nucleic acid identifications to MS/MS spectra. |
|
2 |
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 |
Ocean biodiversity indicators |
from OBIS |
|
2 |
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 |
OGR Informations |
lists information about an OGR supported data source |
|
2 |
OGR2ogr |
converts simple features data between file formats |
|
2 |
OMSSAAdapter |
Annotates MS/MS spectra using OMSSA. |
|
2 |
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 |
OpenPepXLLF |
Tool for protein-protein cross linking with label-free linkers. |
|
3 |
OpenSwathAnalyzer |
Picks peaks and finds features in an SWATH-MS or SRM experiment. |
|
4 |
OpenSwathAssayGenerator |
Generates assays according to different models for a specific TraML |
|
4 |
OpenSwathChromatogramExtractor |
Extract chromatograms (XIC) from a MS2 map file. |
|
3 |
OpenSwathConfidenceScoring |
Compute confidence scores for OpenSwath results |
|
5 |
OpenSwathDecoyGenerator |
Generates decoys according to different models for a specific TraML |
|
5 |
OpenSwathDIAPreScoring |
Scoring spectra using the DIA scores. |
|
4 |
OpenSwathFeatureXMLToTSV |
Converts a featureXML to a mProphet tsv. |
|
4 |
OpenSwathFileSplitter |
Splits SWATH files into n files, each containing one window. |
|
5 |
OpenSwathMzMLFileCacher |
This tool caches the spectra and chromatogram data of an mzML to disk. |
|
4 |
OpenSwathRewriteToFeatureXML |
Combines featureXML and mProphet tsv to FDR filtered featureXML. |
|
5 |
OpenSwathRTNormalizer |
This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. |
|
5 |
OpenSwathWorkflow |
Complete workflow to run OpenSWATH |
|
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 |
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 |
Overlay Images |
for visualization |
|
2 |
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 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.seqs |
calculate uncorrected pairwise distances between sequences |
|
5 |
palindrome |
Looks for inverted repeats in a nucleotide sequence |
|
5 |
Pangolin |
Phylogenetic Assignment of Outbreak Lineages |
|
22 |
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 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 |
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 |
Pathifier |
: Quantify deregulation of pathways in cancer |
|
1 |
Pathview |
for pathway based data integration and visualization |
|
3 |
Pathway Image |
: Draw a KEGG pathway, highlighting specified gene modules |
|
3 |
Pathway Matcher |
PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome. |
|
3 |
patmatdb |
Search a protein sequence with a motif |
|
5 |
PCA |
: Principal Component Analysis of genotype data |
|
3 |
Pca |
Principal Coordinate Analysis for a shared file |
|
6 |
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 |
Pcr.seqs |
Trim sequences |
|
6 |
pdb-to-gro |
converter |
|
1 |
PDBFixer |
to automatically fix a PDB file before performing molecular dynamics simulation |
|
1 |
PEAKachu |
Calls Peaks in CLIP data |
|
3 |
PeakPickerHiRes |
Finds mass spectrometric peaks in profile mass spectra. |
|
4 |
PeakPickerIterative |
Finds mass spectrometric peaks in profile mass spectra. |
|
4 |
PeakPickerWavelet |
Finds mass spectrometric peaks in profile mass spectra. |
|
5 |
Pear |
Paired-End read merger |
|
5 |
pepcoil |
Predicts coiled coil regions |
|
5 |
pepinfo |
Plots simple amino acid properties in parallel |
|
5 |
pepnet |
Displays proteins as a helical net |
|
5 |
PepNovoAdapter |
Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. |
|
2 |
PepPointer |
classify genomic location of peptides |
|
2 |
PepQuery |
Peptide-centric search engine for novel peptide identification and validation. |
|
4 |
pepstats |
Protein statistics |
|
5 |
Peptide Genomic Coordinate |
Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB |
|
2 |
Peptide Prophet |
Calculate Peptide Prophet statistics on search results |
|
2 |
Peptide Shaker |
Perform protein identification using various search engines based on results from SearchGUI |
|
19 |
PeptideIndexer |
Refreshes the protein references for all peptide hits. |
|
6 |
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 |
Percolator |
accurate peptide identification |
|
2 |
PercolatorAdapter |
Facilitate input to Percolator and reintegrate. |
|
2 |
Perform alpha rarefaction |
(alpha_rarefaction) |
|
2 |
Perform Best-subsets Regression |
|
|
2 |
Perform closed-reference OTU picking |
|
|
1 |
Perform jackknifed UPGMA clustering |
and building jackknifed PCoA plots (jackknifed_beta_diversity) |
|
2 |
Perform LDA |
Linear Discriminant Analysis |
|
2 |
Perform metadata association |
on HUMAnN generated table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Perform open-reference OTU picking |
|
|
1 |
Perform open-reference OTU picking |
(pick_open_reference_otus) |
|
2 |
Perform OTU picking |
(pick_otus) |
|
2 |
Perform taxonomy summaries and plots |
(summarize_taxa_through_plots) |
|
2 |
Permutate image |
along an axis |
|
2 |
Personal Cancer Genome Reporter |
|
|
1 |
PfamScan |
search a FASTA sequence against a library of Pfam HMM |
|
1 |
pgma_graphclust |
|
|
3 |
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 |
PhosphoScoring |
Scores potential phosphorylation sites in order to localize the most probable sites. |
|
4 |
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 |
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 Primers |
: Find suitable PCR primers for SNPs |
|
2 |
Pick representative set of sequences |
(pick_rep_set) |
|
2 |
Pileup-to-Interval |
condenses pileup format into ranges of bases |
|
4 |
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 |
pizzly |
- fast fusion detection using kallisto |
|
2 |
PlasFlow |
Prediction of plasmid sequences in metagenomic contigs |
|
1 |
PlasmidFinder |
Plasmid identification in bacteria. |
|
1 |
plasmidSPAdes |
extract and assembly plasmids from WGS data |
|
6 |
plink |
|
|
6 |
Plot |
with scanpy |
|
8 |
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 heatmap of OTU table |
(make_otu_heatmap) |
|
2 |
Plot performance |
per cell in nanopore reads |
|
2 |
Plot signals |
for nanopore reads |
|
2 |
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 |
Plotting tool |
for multiple series and graph types |
|
5 |
PMIDs to PubTator |
binary matrix |
|
1 |
Points to Binary Image |
Converts points to a binary image |
|
1 |
Points to Label |
Points to Label Image |
|
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 |
Polypolish |
Short-read polishing of long-read bacterial genome assemblies |
|
1 |
Population Complexity |
: Evaluate possible numbers of ancestral populations |
|
2 |
Porechop |
adapter trimmer for Oxford Nanopore reads |
|
3 |
Pout2mzid |
add Percolator scoring to mzIdentML |
|
2 |
Pre.cluster |
Remove sequences due to pyrosequencing errors |
|
5 |
PrecursorIonSelector |
PrecursorIonSelector |
|
4 |
PrecursorMassCorrector |
Corrects the precursor entries of MS/MS spectra, by using MS1 information. |
|
5 |
Predict Metagenome |
based on the abundance of OTUs and a functional database |
|
2 |
Predict variant effects |
with VEP |
|
3 |
preg |
Regular expression search of a protein sequence |
|
6 |
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 |
Preprocess |
raw feature vectors into standardized datasets |
|
12 |
Preprocess population data |
for evolution trend analyzes |
|
2 |
Preprocess sentinel 2 data |
read, crop, resample and write it as a raster stack |
|
1 |
Preprocessing |
|
|
4 |
Presence-absence and abundance |
Community abundance map, presence barplot and rarefaction curves |
|
1 |
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.design |
identify sequence fragments that are specific to particular OTUs |
|
5 |
primersearch |
Searches DNA sequences for matches with primer pairs |
|
5 |
Principal component analysis |
with scikit-learn |
|
3 |
Principal Component Analysis |
|
|
1 |
PRINSEQ |
to process quality of sequences |
|
5 |
ProbMetab Tool |
Wrapper function for ProbMetab R package. |
|
2 |
Process Scans (and SIM-Stitch) |
- Read, filter and average MS scans |
|
2 |
Process single-cell intensities |
Options to correct for exposure time, autofluorescence subtraction, or compute signal-to-background ratio. |
|
1 |
proFIA |
Preprocessing of FIA-HRMS data |
|
2 |
Profile Annotations |
for a set of genomic intervals |
|
1 |
progressiveMauve |
constructs multiple genome alignments |
|
3 |
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 |
prot-scriber |
Protein annotation of short human readable descriptions |
|
3 |
Protease prediction |
based on cleavage sites |
|
3 |
Protein Database Downloader |
|
|
6 |
Protein Prophet |
Calculate Protein Prophet statistics on search results |
|
2 |
ProteinInference |
Protein inference based on the number of identified peptides. |
|
4 |
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 |
ProteinQuantifier |
Compute peptide and protein abundances |
|
4 |
ProteinResolver |
protein inference |
|
4 |
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 |
PSMFeatureExtractor |
Computes extra features for each input PSM. |
|
5 |
psortb |
Determines sub-cellular localisation of bacterial/archaeal protein sequences |
|
5 |
PTModel |
Trains a model for the prediction of proteotypic peptides from a training set. |
|
4 |
PTPredict |
predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel |
|
2 |
PubChem Assay Downloader |
as canonical SMILES |
|
3 |
PubChem Download |
as canonical SMILES |
|
3 |
PubMed query |
download a defined number of abstracts or PMIDs from PubMed |
|
1 |
PureCLIP |
- HMM based peak caller designed for eCLIP/iCLIP data |
|
2 |
Purge overlaps |
and haplotigs in an assembly based on read depth (purge_dups) |
|
6 |
Pycoqc |
|
|
1 |
pyGenomeTracks |
plot genomic data tracks |
|
12 |
PyIron |
meta tools |
|
1 |
PyMuonSuite AIRSS Cluster |
run clustering for optimised structures |
|
2 |
PyMuonSuite AIRSS Configure |
define AIRSS parameters |
|
2 |
PyMuonSuite AIRSS DFTB+ Optimise |
run DFTB+ optimisation |
|
2 |
PyMuonSuite AIRSS Generate |
generate muonated structures |
|
2 |
PyMuonSuite AIRSS UEP Optimise |
run UEP optimisation |
|
2 |
PyMuonSuite Phonons |
calculate phonons using ASE and DFTB+ |
|
2 |
PyMuonSuite Symmetry |
generate Wyckoff points symmetry report |
|
2 |
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 |
pysradb search |
sequence metadata from SRA/ENA |
|
2 |
pyteomics |
convert mztab to tabular |
Conversion
|
1 |
QCCalculator |
Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. |
|
5 |
QCEmbedder |
Attaches a table or an image to a given qc parameter. |
|
4 |
QCExporter |
Will extract several qp from several run/sets in a tabular format. |
|
4 |
QCExtractor |
Extracts a table attachment to a given qc parameter. |
|
4 |
QCImporter |
Imports tables with quality control parameters into qcml files. |
|
4 |
QCMerger |
Merges two qcml files together. |
|
5 |
QCShrinker |
This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. |
|
4 |
QECB-Dissimilarity |
indicator |
|
1 |
qiime2 alignment mafft |
De novo multiple sequence alignment with MAFFT |
|
2 |
qiime2 alignment mafft-add |
Add sequences to multiple sequence alignment with MAFFT. |
|
2 |
qiime2 alignment mask |
Positional conservation and gap filtering. |
|
2 |
qiime2 composition add-pseudocount |
Add pseudocount to table |
|
2 |
qiime2 composition ancom |
Apply ANCOM to identify features that differ in abundance. |
|
2 |
qiime2 composition ancombc |
Analysis of Composition of Microbiomes with Bias Correction |
|
1 |
qiime2 composition tabulate |
View tabular output from ANCOM-BC. |
|
1 |
qiime2 cutadapt demux-paired |
Demultiplex paired-end sequence data with barcodes in-sequence. |
|
2 |
qiime2 cutadapt demux-single |
Demultiplex single-end sequence data with barcodes in-sequence. |
|
2 |
qiime2 cutadapt trim-paired |
Find and remove adapters in demultiplexed paired-end sequences. |
|
2 |
qiime2 cutadapt trim-single |
Find and remove adapters in demultiplexed single-end sequences. |
|
2 |
qiime2 dada2 denoise-ccs |
Denoise and dereplicate single-end Pacbio CCS |
|
2 |
qiime2 dada2 denoise-paired |
Denoise and dereplicate paired-end sequences |
|
2 |
qiime2 dada2 denoise-pyro |
Denoise and dereplicate single-end pyrosequences |
|
2 |
qiime2 dada2 denoise-single |
Denoise and dereplicate single-end sequences |
|
2 |
qiime2 deblur denoise-16S |
Deblur sequences using a 16S positive filter. |
|
1 |
qiime2 deblur denoise-other |
Deblur sequences using a user-specified positive filter. |
|
2 |
qiime2 deblur visualize-stats |
Visualize Deblur stats per sample. |
|
2 |
qiime2 demux emp-paired |
Demultiplex paired-end sequence data generated with the EMP protocol. |
|
2 |
qiime2 demux emp-single |
Demultiplex sequence data generated with the EMP protocol. |
|
2 |
qiime2 demux filter-samples |
Filter samples out of demultiplexed data. |
|
2 |
qiime2 demux subsample-paired |
Subsample paired-end sequences without replacement. |
|
2 |
qiime2 demux subsample-single |
Subsample single-end sequences without replacement. |
|
2 |
qiime2 demux summarize |
Summarize counts per sample. |
|
2 |
qiime2 diversity adonis |
adonis PERMANOVA test for beta group significance |
|
2 |
qiime2 diversity alpha |
Alpha diversity |
|
2 |
qiime2 diversity alpha-correlation |
Alpha diversity correlation |
|
2 |
qiime2 diversity alpha-group-significance |
Alpha diversity comparisons |
|
2 |
qiime2 diversity alpha-phylogenetic |
Alpha diversity (phylogenetic) |
|
2 |
qiime2 diversity alpha-rarefaction |
Alpha rarefaction curves |
|
2 |
qiime2 diversity beta |
Beta diversity |
|
2 |
qiime2 diversity beta-correlation |
Beta diversity correlation |
|
2 |
qiime2 diversity beta-group-significance |
Beta diversity group significance |
|
2 |
qiime2 diversity beta-phylogenetic |
Beta diversity (phylogenetic) |
|
2 |
qiime2 diversity beta-rarefaction |
Beta diversity rarefaction |
|
2 |
qiime2 diversity bioenv |
bioenv |
|
2 |
qiime2 diversity core-metrics |
Core diversity metrics (non-phylogenetic) |
|
2 |
qiime2 diversity core-metrics-phylogenetic |
Core diversity metrics (phylogenetic and non-phylogenetic) |
|
2 |
qiime2 diversity filter-distance-matrix |
Filter samples from a distance matrix. |
|
2 |
qiime2 diversity mantel |
Apply the Mantel test to two distance matrices |
|
2 |
qiime2 diversity pcoa |
Principal Coordinate Analysis |
|
2 |
qiime2 diversity pcoa-biplot |
Principal Coordinate Analysis Biplot |
|
2 |
qiime2 diversity procrustes-analysis |
Procrustes Analysis |
|
2 |
qiime2 diversity tsne |
t-distributed stochastic neighbor embedding |
|
2 |
qiime2 diversity umap |
Uniform Manifold Approximation and Projection |
|
2 |
qiime2 diversity-lib alpha-passthrough |
Alpha Passthrough (non-phylogenetic) |
|
2 |
qiime2 diversity-lib beta-passthrough |
Beta Passthrough (non-phylogenetic) |
|
2 |
qiime2 diversity-lib beta-phylogenetic-meta-passthrough |
Beta Phylogenetic Meta Passthrough |
|
2 |
qiime2 diversity-lib beta-phylogenetic-passthrough |
Beta Phylogenetic Passthrough |
|
2 |
qiime2 diversity-lib bray-curtis |
Bray-Curtis Dissimilarity |
|
2 |
qiime2 diversity-lib faith-pd |
Faith's Phylogenetic Diversity |
|
2 |
qiime2 diversity-lib jaccard |
Jaccard Distance |
|
2 |
qiime2 diversity-lib observed-features |
Observed Features |
|
2 |
qiime2 diversity-lib pielou-evenness |
Pielou's Evenness |
|
2 |
qiime2 diversity-lib shannon-entropy |
Shannon's Entropy |
|
2 |
qiime2 diversity-lib unweighted-unifrac |
Unweighted Unifrac |
|
2 |
qiime2 diversity-lib weighted-unifrac |
Weighted Unifrac |
|
2 |
qiime2 emperor biplot |
Visualize and Interact with Principal Coordinates Analysis Biplot |
|
2 |
qiime2 emperor plot |
Visualize and Interact with Principal Coordinates Analysis Plots |
|
2 |
qiime2 emperor procrustes-plot |
Visualize and Interact with a procrustes plot |
|
2 |
qiime2 feature-classifier blast |
BLAST+ local alignment search. |
|
2 |
qiime2 feature-classifier classify-consensus-blast |
BLAST+ consensus taxonomy classifier |
|
2 |
qiime2 feature-classifier classify-consensus-vsearch |
VSEARCH-based consensus taxonomy classifier |
|
2 |
qiime2 feature-classifier classify-hybrid-vsearch-sklearn |
ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier |
|
2 |
qiime2 feature-classifier classify-sklearn |
Pre-fitted sklearn-based taxonomy classifier |
|
2 |
qiime2 feature-classifier extract-reads |
Extract reads from reference sequences. |
|
2 |
qiime2 feature-classifier find-consensus-annotation |
Find consensus among multiple annotations. |
|
2 |
qiime2 feature-classifier fit-classifier-naive-bayes |
Train the naive_bayes classifier |
|
2 |
qiime2 feature-classifier fit-classifier-sklearn |
Train an almost arbitrary scikit-learn classifier |
|
2 |
qiime2 feature-classifier vsearch-global |
VSEARCH global alignment search |
|
2 |
qiime2 feature-table core-features |
Identify core features in table |
|
2 |
qiime2 feature-table filter-features |
Filter features from table |
|
2 |
qiime2 feature-table filter-features-conditionally |
Filter features from a table based on abundance and prevalence |
|
2 |
qiime2 feature-table filter-samples |
Filter samples from table |
|
2 |
qiime2 feature-table filter-seqs |
Filter features from sequences |
|
2 |
qiime2 feature-table group |
Group samples or features by a metadata column |
|
2 |
qiime2 feature-table heatmap |
Generate a heatmap representation of a feature table |
|
2 |
qiime2 feature-table merge |
Combine multiple tables |
|
2 |
qiime2 feature-table merge-seqs |
Combine collections of feature sequences |
|
2 |
qiime2 feature-table merge-taxa |
Combine collections of feature taxonomies |
|
2 |
qiime2 feature-table presence-absence |
Convert to presence/absence |
|
2 |
qiime2 feature-table rarefy |
Rarefy table |
|
2 |
qiime2 feature-table relative-frequency |
Convert to relative frequencies |
|
2 |
qiime2 feature-table rename-ids |
Renames sample or feature ids in a table |
|
2 |
qiime2 feature-table subsample |
Subsample table |
|
2 |
qiime2 feature-table summarize |
Summarize table |
|
2 |
qiime2 feature-table tabulate-seqs |
View sequence associated with each feature |
|
2 |
qiime2 feature-table transpose |
Transpose a feature table. |
|
2 |
qiime2 fragment-insertion classify-otus-experimental |
Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. |
|
2 |
qiime2 fragment-insertion filter-features |
Filter fragments in tree from table. |
|
2 |
qiime2 fragment-insertion sepp |
Insert fragment sequences using SEPP into reference phylogenies. |
|
2 |
qiime2 gneiss assign-ids |
Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. |
|
2 |
qiime2 gneiss correlation-clustering |
Hierarchical clustering using feature correlation. |
|
2 |
qiime2 gneiss dendrogram-heatmap |
Dendrogram heatmap. |
|
2 |
qiime2 gneiss gradient-clustering |
Hierarchical clustering using gradient information. |
|
2 |
qiime2 gneiss ilr-hierarchical |
Isometric Log-ratio Transform applied to a hierarchical clustering |
|
2 |
qiime2 gneiss ilr-phylogenetic |
Isometric Log-ratio Transform applied to a phylogenetic tree |
|
2 |
qiime2 gneiss ilr-phylogenetic-differential |
Differentially abundant Phylogenetic Log Ratios. |
|
2 |
qiime2 gneiss ilr-phylogenetic-ordination |
Ordination through a phylogenetic Isometric Log Ratio transform. |
|
2 |
qiime2 longitudinal anova |
ANOVA test |
|
2 |
qiime2 longitudinal feature-volatility |
Feature volatility analysis |
|
2 |
qiime2 longitudinal first-differences |
Compute first differences or difference from baseline between sequential states |
|
2 |
qiime2 longitudinal first-distances |
Compute first distances or distance from baseline between sequential states |
|
2 |
qiime2 longitudinal linear-mixed-effects |
Linear mixed effects modeling |
|
2 |
qiime2 longitudinal maturity-index |
Microbial maturity index prediction. |
|
2 |
qiime2 longitudinal nmit |
Nonparametric microbial interdependence test |
|
2 |
qiime2 longitudinal pairwise-differences |
Paired difference testing and boxplots |
|
2 |
qiime2 longitudinal pairwise-distances |
Paired pairwise distance testing and boxplots |
|
2 |
qiime2 longitudinal plot-feature-volatility |
Plot longitudinal feature volatility and importances |
|
2 |
qiime2 longitudinal volatility |
Generate interactive volatility plot |
|
2 |
qiime2 metadata distance-matrix |
Create a distance matrix from a numeric Metadata column |
|
2 |
qiime2 metadata shuffle-groups |
Shuffle values in a categorical sample metadata column. |
|
2 |
qiime2 metadata tabulate |
Interactively explore Metadata in an HTML table |
|
2 |
qiime2 phylogeny align-to-tree-mafft-fasttree |
Build a phylogenetic tree using fasttree and mafft alignment |
|
2 |
qiime2 phylogeny align-to-tree-mafft-iqtree |
Build a phylogenetic tree using iqtree and mafft alignment. |
|
2 |
qiime2 phylogeny align-to-tree-mafft-raxml |
Build a phylogenetic tree using raxml and mafft alignment. |
|
2 |
qiime2 phylogeny fasttree |
Construct a phylogenetic tree with FastTree. |
|
2 |
qiime2 phylogeny filter-table |
Remove features from table if they're not present in tree. |
|
2 |
qiime2 phylogeny filter-tree |
Remove features from tree based on metadata |
|
2 |
qiime2 phylogeny iqtree |
Construct a phylogenetic tree with IQ-TREE. |
|
2 |
qiime2 phylogeny iqtree-ultrafast-bootstrap |
Construct a phylogenetic tree with IQ-TREE with bootstrap supports. |
|
2 |
qiime2 phylogeny midpoint-root |
Midpoint root an unrooted phylogenetic tree. |
|
2 |
qiime2 phylogeny raxml |
Construct a phylogenetic tree with RAxML. |
|
2 |
qiime2 phylogeny raxml-rapid-bootstrap |
Construct a phylogenetic tree with bootstrap supports using RAxML. |
|
2 |
qiime2 phylogeny robinson-foulds |
Calculate Robinson-Foulds distance between phylogenetic trees. |
|
2 |
qiime2 quality-control bowtie2-build |
Build bowtie2 index from reference sequences. |
|
2 |
qiime2 quality-control evaluate-composition |
Evaluate expected vs. observed taxonomic composition of samples |
|
2 |
qiime2 quality-control evaluate-seqs |
Compare query (observed) vs. reference (expected) sequences. |
|
2 |
qiime2 quality-control evaluate-taxonomy |
Evaluate expected vs. observed taxonomic assignments |
|
2 |
qiime2 quality-control exclude-seqs |
Exclude sequences by alignment |
|
2 |
qiime2 quality-control filter-reads |
Filter demultiplexed sequences by alignment to reference database. |
|
2 |
qiime2 quality-filter q-score |
Quality filter based on sequence quality scores. |
|
2 |
qiime2 sample-classifier classify-samples |
Train and test a cross-validated supervised learning classifier. |
|
2 |
qiime2 sample-classifier classify-samples-from-dist |
Run k-nearest-neighbors on a labeled distance matrix. |
|
2 |
qiime2 sample-classifier classify-samples-ncv |
Nested cross-validated supervised learning classifier. |
|
2 |
qiime2 sample-classifier confusion-matrix |
Make a confusion matrix from sample classifier predictions. |
|
2 |
qiime2 sample-classifier fit-classifier |
Fit a supervised learning classifier. |
|
2 |
qiime2 sample-classifier fit-regressor |
Fit a supervised learning regressor. |
|
2 |
qiime2 sample-classifier heatmap |
Generate heatmap of important features. |
|
2 |
qiime2 sample-classifier metatable |
Convert (and merge) positive numeric metadata (in)to feature table. |
|
2 |
qiime2 sample-classifier predict-classification |
Use trained classifier to predict target values for new samples. |
|
2 |
qiime2 sample-classifier predict-regression |
Use trained regressor to predict target values for new samples. |
|
2 |
qiime2 sample-classifier regress-samples |
Train and test a cross-validated supervised learning regressor. |
|
2 |
qiime2 sample-classifier regress-samples-ncv |
Nested cross-validated supervised learning regressor. |
|
2 |
qiime2 sample-classifier scatterplot |
Make 2D scatterplot and linear regression of regressor predictions. |
|
2 |
qiime2 sample-classifier split-table |
Split a feature table into training and testing sets. |
|
2 |
qiime2 sample-classifier summarize |
Summarize parameter and feature extraction information for a trained estimator. |
|
2 |
qiime2 taxa barplot |
Visualize taxonomy with an interactive bar plot |
|
2 |
qiime2 taxa collapse |
Collapse features by their taxonomy at the specified level |
|
2 |
qiime2 taxa filter-seqs |
Taxonomy-based feature sequence filter. |
|
2 |
qiime2 taxa filter-table |
Taxonomy-based feature table filter. |
|
2 |
qiime2 tools export |
Export data from a QIIME 2 artifact |
|
2 |
qiime2 tools import |
Import data into a QIIME 2 artifact |
|
2 |
qiime2 vsearch cluster-features-closed-reference |
Closed-reference clustering of features. |
|
2 |
qiime2 vsearch cluster-features-de-novo |
De novo clustering of features. |
|
2 |
qiime2 vsearch cluster-features-open-reference |
Open-reference clustering of features. |
|
2 |
qiime2 vsearch dereplicate-sequences |
Dereplicate sequences. |
|
2 |
qiime2 vsearch fastq-stats |
Fastq stats with vsearch. |
|
2 |
qiime2 vsearch merge-pairs |
Merge paired-end reads. |
|
1 |
qiime2 vsearch uchime-denovo |
De novo chimera filtering with vsearch. |
|
2 |
qiime2 vsearch uchime-ref |
Reference-based chimera filtering with vsearch. |
|
2 |
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 |
QualityControl |
Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get. |
|
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 Tabular |
using sqlite sql |
|
8 |
Racon |
Consensus module for raw de novo DNA assembly of long uncorrected reads |
|
8 |
RagTag |
reference-guided scaffolding of draft genomes |
|
2 |
Ramachandran Analysis |
- Ramachandran plot for proteins |
|
2 |
Ramachandran Plots |
- calculate and plot the distribution of two dihedrals in a trajectory |
|
4 |
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 |
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 |
RDConf: Low-energy ligand conformer search |
using RDKit |
|
1 |
RDF Analysis |
- Radial Distribution Function between two atoms |
|
4 |
rDock cavity definition |
- generate the active site definition needed for rDock docking |
|
2 |
rDock docking |
- perform protein-ligand docking with rDock |
|
6 |
rDock docking |
using the sdsort provided with rDock |
|
3 |
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 |
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 NVC |
to check the nucleotide composition bias |
|
10 |
Read Quality |
determines Phred quality score |
|
10 |
Realign reads |
with LoFreq viterbi |
|
5 |
Rebase GFF3 features |
against parent features |
|
2 |
Recentrifuge |
Robust comparative analysis and contamination removal for metagenomics |
Statistical calculation
Taxonomic classification
|
3 |
Red |
repeat masking |
|
2 |
Reduce |
a joined HUMAnN table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Reduce |
a HUMAnN2 generated table |
|
4 |
Regex Find And Replace |
|
|
5 |
Regex Replace |
Regular Expression replacement using the Python re module |
|
1 |
Register Account |
with Apollo |
|
7 |
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 |
Remarkable Intervals |
: Find high-scoring runs of SNPs |
|
3 |
Remove 3'-end nts |
from FASTQ |
|
3 |
Remove beginning |
of a file |
|
1 |
Remove columns |
by heading |
|
2 |
Remove confounders |
with scanpy |
|
7 |
Remove counterions and fragments |
from a library of compounds |
|
7 |
Remove counterions and fragments |
|
|
2 |
Remove duplicated molecules |
from a library of compounds |
|
5 |
Remove protonation state |
of every atom |
|
6 |
Remove sequencing artifacts |
|
|
5 |
Remove small molecules |
from a library of compounds |
|
5 |
Remove spurious |
crosslinking events |
|
3 |
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 |
remuRNA |
Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation |
|
1 |
Rename |
features of a HUMAnN2 generated table |
|
4 |
Rename features |
of a HUMAnN generated table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
Rename OME-TIFF Channels |
Change the channel names in the XML metadata of OME-TIFF images |
|
1 |
Rename sequences |
|
|
5 |
Rename.seqs |
Rename sequences by concatenating the group name |
|
2 |
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 chromosome names |
in a tabular dataset using a mapping table |
|
1 |
Replace column |
by values which are defined in a convert file |
|
2 |
Replace Text |
in a specific column |
|
11 |
Replace Text |
in entire line |
|
11 |
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 |
Resampling |
- determine per-gene p-values |
|
5 |
Resize coordinate window |
of GFF data |
|
3 |
Restore Attributes |
: Fill in missing properties for a gd_snp or gd_genotype dataset |
|
3 |
Retrieve a run report |
|
|
2 |
Retrieve an analysis report |
|
|
2 |
Retrieve Data |
from Apollo into Galaxy |
|
8 |
Retrieve ENA data |
(other than taxon and project) |
|
2 |
Retrieve ENA taxon data |
|
|
2 |
Retrieve JBrowse |
for an organism, from Apollo |
|
8 |
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 |
RGCCA |
performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals. |
Analysis
Correlation
Visualisation
|
2 |
ribotaper part 1: creation of annotation files |
|
|
4 |
ribotaper part 2: metagene analysis for P-sites definition |
|
|
4 |
ribotaper part 3: ribosome profiling |
|
|
4 |
riboWaltz |
calculation of optimal P-site offsets and diagnostic analysis |
Translation initiation site prediction
|
1 |
riboWaltz-plot |
visual inspection of ribosome profiling data |
Translation initiation site prediction
|
1 |
RmDup |
remove PCR duplicates |
|
5 |
RMSD Analysis |
using Bio3D |
|
2 |
RMSF Analysis |
using Bio3D |
|
2 |
RNA fragment size |
calculates the fragment size for each gene/transcript |
|
8 |
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 |
|
2 |
RNABOB |
Fast Pattern searching for RNA secondary structures |
|
2 |
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 |
RNADigestor |
Digests an RNA sequence database in-silico. |
|
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 |
|
4 |
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 |
RNALfoldz |
calculates locally stable secondary structures of RNA |
|
1 |
RNAlien |
Unsupervised covariance model construction from a single input sequence |
|
1 |
RNAMassCalculator |
Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences |
|
2 |
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 |
RNAplot |
Draw RNA Secondary Structures |
|
1 |
rnaQUAST |
A Quality Assessment Tool for De Novo Transcriptome Assemblies |
|
3 |
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 |
RNPxl |
Tool for RNP cross linking experiment analysis. |
|
2 |
RNPxlSearch |
Annotate RNA to peptide crosslinks in MS/MS spectra. |
|
4 |
RNPxlXICFilter |
Remove MS2 spectra from treatment based on the fold change between control and treatment. |
|
5 |
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 |
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 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 |
RTEvaluation |
Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. |
|
5 |
RTModel |
Trains a model for the retention time prediction of peptides from a training set. |
|
4 |
RTPredict |
Predicts retention times for peptides using a model trained by RTModel. |
|
2 |
rtsne |
|
|
1 |
Run a core set of QIIME diversity analyses |
(core_diversity_analyses) |
|
2 |
Run join_paired_ends on multiple files |
(multiple_join_paired_ends) |
|
2 |
Run OpenDUck |
steered molecular dynamics runs |
|
1 |
Run SCCAF |
to assess and optimise clustering |
|
2 |
Run split_libraries_fastq on multiple files |
(multiple_split_libraries_fastq) |
|
2 |
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 |
s3segmenter |
single cell (nuclei and cytoplasm) label masks. |
|
1 |
Sailfish |
transcript quantification from RNA-seq data |
|
4 |
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-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 |
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 |
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 |
SaveImages |
or movie files |
|
2 |
SC3 Calculate Consensus |
from multiple runs of k-means clustering |
|
1 |
SC3 Calculate Distances |
between cells |
|
1 |
SC3 Calculate Transformations |
of distances using PCA and graph Laplacian |
|
1 |
SC3 DiffExp |
calculates DE genes, marker genes and cell outliers |
|
1 |
SC3 Estimate |
the number of clusters for k-means clustering |
|
1 |
SC3 K-Means |
perform k-means clustering |
|
1 |
SC3 Prepare |
a sc3 SingleCellExperiment object |
|
1 |
Scale Image |
Scales image |
|
3 |
scanMotifGenomeWide |
|
|
1 |
Scanpy BBKNN |
batch-balanced K-nearest neighbours |
|
6 |
Scanpy ComBat |
adjust expression for variables that might introduce batch effect |
|
6 |
Scanpy ComputeGraph |
to derive kNN graph |
|
16 |
Scanpy DiffusionMap |
calculate diffusion components |
|
11 |
Scanpy DPT |
diffusion pseudotime inference |
|
11 |
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 MNN |
correct batch effects by matching mutual nearest neighbors |
|
6 |
Scanpy NormaliseData |
to make all cells having the same total expression |
|
14 |
Scanpy PAGA |
trajectory inference |
|
10 |
Scanpy ParameterIterator |
produce an iteration over a defined parameter |
|
5 |
Scanpy Plot Scrublet |
visualise multiplet scoring distribution |
|
2 |
Scanpy PlotEmbed |
visualise cell embeddings |
|
12 |
Scanpy PlotTrajectory |
visualise cell trajectories |
|
11 |
Scanpy Read10x |
into hdf5 object handled by scanpy |
|
13 |
Scanpy RegressOut |
variables that might introduce batch effect |
|
10 |
Scanpy RunFDG |
visualise cell clusters using force-directed graph |
|
11 |
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 |
Scanpy Scrublet |
remove multiplets from annData objects with Scrublet |
|
2 |
Scater CalculateCPM |
from raw counts |
|
1 |
Scater CalculateQcMetrics |
based on expression values and experiment information |
|
1 |
Scater DetectOutlier |
cells based on expression metrics |
|
1 |
Scater read 10x data |
Loads 10x data into a serialized scater R object |
|
1 |
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 |
SCCAF Assesment |
runs an assesment of an SCCAF optimisation result or an existing clustering. |
|
2 |
SCCAF Assesment Merger |
brings together distributed assesments. |
|
2 |
SCCAF mulitple regress out |
with multiple categorical keys on an AnnData object. |
|
1 |
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 |
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 |
Scmap cell projection |
searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets. |
|
6 |
Scmap cluster projection |
projects one dataset to another |
|
5 |
Scmap get standard output |
Create final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package |
|
3 |
Scmap index cells |
creates a cell index for a dataset to enable fast approximate nearest neighbour search |
|
7 |
Scmap index clusters |
calculates centroids of each cell type and merges them into a single table |
|
6 |
Scmap pre-process |
Pre-process SCE object before running downstream analysis |
|
2 |
Scmap select features |
finds the most informative features (genes/transcripts) for projection. |
|
5 |
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 |
scPipe |
- preprocessing pipeline for single cell RNA-seq |
|
4 |
Scpred - get output in standard format |
This method allows to export predicted labels in a standardised format, simplifying downstream analyses. |
|
4 |
Scpred eigen-decompose |
Perform matrix eigen-decomposition; initialize object of scPred class |
|
3 |
ScPred feature space |
Get feature space for training matrix |
|
4 |
Scpred pre-process |
Pre-process input dataset (no train/test split) |
|
1 |
Scpred predict |
Make cell type predictions using trained model. |
|
4 |
Scpred train |
Train classification model |
|
4 |
Scpred train-test split |
CPM normalise and partition into train/test data |
|
3 |
scran_normalize |
Normalize raw counts expression values using deconvolution size factors |
|
1 |
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 Fingerprint |
- extract fingerprints from sdf file metadata |
|
5 |
SEACR |
for sparse enrichment analysis |
|
1 |
Search ChEMBL database |
for compounds which are similar to a SMILES string |
|
6 |
Search ENA data |
given a query |
|
2 |
Search engine output to Pin converter |
to create Percolator input files |
|
2 |
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 |
SeedListGenerator |
Generates seed lists for feature detection. |
|
3 |
segemehl |
short read mapping with gaps |
|
3 |
segmentation-fold |
RNA-Folding including predefined segments including K-turns |
|
4 |
SegMetrics |
image segmentation and object detection performance measures |
|
1 |
Select |
lines that match an expression |
Filtering
|
3 |
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 random lines |
from a file |
|
2 |
Select Sequences |
Tool to select representative sequences from a multiple sequence alignment. |
|
2 |
SemanticValidator |
SemanticValidator for semantically validating certain XML files. |
|
4 |
SemiBin |
for Semi-supervised Metagenomic Binning |
|
1 |
SemiBin: Concatenate fasta files |
for multi-sample binning |
|
1 |
SemiBin: Contig annotations |
|
|
1 |
SemiBin: Generate sequence features |
(kmer and abundance) as training data for semi-supervised deep learning model training |
|
1 |
SemiBin: Group the contigs |
into bins |
|
1 |
SemiBin: Train |
the semi-supervised deep learning model |
|
1 |
Send to cloud |
|
|
1 |
Sens.spec |
Determine the quality of OTU assignment |
|
6 |
Separate pgSnp alleles |
into columns |
|
1 |
Seq.error |
assess error rates in sequencing data |
|
5 |
seq2HLA |
HLA genotype and expression from RNA-seq |
|
2 |
SeqKit fx2tab |
convert FASTA/Q to tabular |
|
3 |
SeqKit locate |
subsequences/motifs, mismatch allowed |
|
2 |
SeqKit statistics |
of FASTA/Q files |
|
3 |
seqmatchall |
All-against-all comparison of a set of sequences |
|
5 |
seqret |
Reads and writes sequences |
|
5 |
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 converter |
for various sequence formats |
|
1 |
Sequence Logo |
generator for fasta (eg Clustal alignments) |
|
2 |
SequenceCoverageCalculator |
Prints information about idXML files. |
|
5 |
seqwish |
Alignment to variation graph inducer |
|
7 |
Seurat |
- toolkit for exploration of single-cell RNA-seq data |
|
12 |
Seurat CreateSeuratObject |
create a Seurat object |
|
1 |
Seurat Export2CellBrowser |
produces files for UCSC CellBrowser import. |
|
5 |
Seurat FilterCells |
filter cells in a Seurat object |
|
5 |
Seurat FindClusters |
find clusters of cells |
|
5 |
Seurat FindMarkers |
find markers (differentially expressed genes) |
|
5 |
Seurat FindNeighbours |
constructs a Shared Nearest Neighbor (SNN) Graph |
|
4 |
Seurat FindVariableGenes |
identify variable genes |
|
5 |
Seurat NormaliseData |
normalise data |
|
5 |
Seurat Plot dimension reduction |
graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class. |
|
5 |
Seurat Read10x |
Loads Tabular or 10x data into a serialized seurat R object |
|
5 |
Seurat RunPCA |
run a PCA dimensionality reduction |
|
5 |
Seurat RunTSNE |
run t-SNE dimensionality reduction |
|
5 |
Seurat ScaleData |
scale and center genes |
|
5 |
SFF converter |
|
|
1 |
Sffinfo |
Summarize the quality of sequences |
|
5 |
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 |
SimpleSearchEngine |
Annotates MS/MS spectra using SimpleSearchEngine. |
|
4 |
SINA |
reference based multiple sequence alignment |
|
5 |
SIRIUS-CSI:FingerID |
is used to identify metabolites using single and tandem mass spectrometry |
|
7 |
SiriusAdapter |
Tool for metabolite identification using single and tandem mass spectrometry |
|
4 |
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 |
smi-to-mol |
converter |
|
2 |
smi-to-smi |
converter |
|
2 |
smina |
Scoring and Minimization with AutoDock Vina |
|
1 |
Smooth |
|
|
2 |
Smudgeplot |
inference of ploidy and heterozygosity structure using whole genome sequencing |
|
1 |
sniffles |
Structural variation caller using third generation sequencing |
|
1 |
snipit |
Summarise snps relative to a reference sequence |
|
2 |
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 |
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 |
SnpSift Annotate |
SNPs from dbSnp |
|
9 |
SnpSift CaseControl |
Count samples are in 'case' and 'control' groups. |
|
9 |
SnpSift dbNSFP |
Add Annotations from dbNSFP and similar annotation DBs |
|
2 |
SnpSift dbNSFP |
Add annotations from dbNSFP or similar annotation DBs |
|
4 |
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 |
socru |
Calculate the order and orientation of complete bacterial genomes |
|
1 |
SOPRA with prebuilt contigs |
for Illumina libraries |
|
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 Column Order |
by heading |
|
1 |
Sort.seqs |
put sequences in different files in the same order |
|
6 |
SortSam |
sort SAM/BAM dataset |
|
14 |
SPAdes |
genome assembler for genomes of regular and single-cell projects |
Genome assembly
|
16 |
Spaln: align cDNA or Protein to genome |
Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. |
|
5 |
Sparse Matrix Functions |
for manipulating 2-D Scipy sparse numeric data |
|
11 |
Spatial coordinates anonymization |
without loss of the spatial relationships |
|
1 |
Species tree generator |
from a list of species using the ETE Toolkit |
|
1 |
Specify Individuals |
: Define a collection of individuals from a gd_snp dataset |
|
3 |
SpecLibCreator |
Creates an MSP formatted spectral library. |
|
4 |
SpecLibSearcher |
Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. |
|
3 |
SpectraFilterBernNorm |
Applies thresholdfilter to peak spectra. |
|
4 |
SpectraFilterMarkerMower |
Applies thresholdfilter to peak spectra. |
|
4 |
SpectraFilterNLargest |
Applies thresholdfilter to peak spectra. |
|
5 |
SpectraFilterNormalizer |
Normalizes intensity of peak spectra. |
|
5 |
SpectraFilterParentPeakMower |
Applies thresholdfilter to peak spectra. |
|
4 |
SpectraFilterScaler |
Applies thresholdfilter to peak spectra. |
|
4 |
SpectraFilterSqrtMower |
Applies thresholdfilter to peak spectra. |
|
4 |
SpectraFilterThresholdMower |
Applies thresholdfilter to peak spectra. |
|
5 |
SpectraFilterWindowMower |
Applies thresholdfilter to peak spectra. |
|
4 |
SpectraMerger |
Merges spectra (each MS level separately), increasing S/N ratios. |
|
5 |
SpectraSTSearchAdapter |
Interface to the SEARCH Mode of the SpectraST executable |
|
4 |
Spectrophores search |
- similarity search based on 1D chemical features |
|
5 |
Spectrophores(TM) search: |
similarity search based on 1D chemical features |
|
2 |
Split |
a merged HUMAnN table |
Nucleic acid sequence analysis
Phylogenetic analysis
|
2 |
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 by Mapped |
|
|
2 |
Split BAM by Paired/Single End |
|
|
2 |
Split BAM by Reference |
into dataset list collection |
|
2 |
Split BAM by Tag |
into dataset list collection |
|
2 |
Split Dataset |
into training and test subsets |
|
6 |
Split Fasta |
files into a collection |
|
3 |
Split fastq libraries |
to performs demultiplexing of Fastq sequence data (split_libraries_fastq) |
|
2 |
Split file |
according to the values of a column |
|
4 |
Split file |
to dataset collection |
|
7 |
Split Labelmap |
|
|
1 |
Split libraries |
according to barcodes specified in mapping file (split_libraries) |
|
2 |
Split MAF blocks |
by Species |
|
1 |
Split objects |
Split binary image by using watershed |
|
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 |
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 |
Squidpy Graph and Plotting |
for spatial analysis |
|
1 |
sRNAPipe |
In-depth study of small RNA |
|
4 |
SRST2 |
Short Read Sequence Typing for Bacterial Pathogens |
|
2 |
SSAKE |
short DNA sequences assembler |
|
1 |
ssHMM |
- RNA sequence-structure motif finder |
|
1 |
Stacking Ensembles |
builds stacking, voting ensemble models with numerous base options |
|
8 |
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 |
Starting Modules |
load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups) |
|
2 |
Statistical hypothesis testing |
computes several descriptive statistics |
|
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 |
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 |
Structure |
using multi-locus genotype data to investigate population structure |
|
2 |
Structure to GSPAN |
|
|
3 |
Sub-sample sequences files |
e.g. to reduce coverage |
|
4 |
Sub.sample |
Create a sub sample |
|
5 |
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 |
Summarize taxa |
and store results in a new table or appended to an existing mapping file (summarize_taxa) |
|
2 |
Summarize taxonomy |
|
|
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 |
|
2 |
Support vector machines (SVMs) |
for classification |
|
12 |
SvmTheoreticalSpectrumGeneratorTrainer |
Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator |
|
5 |
Switch axis coordinates |
Switches the axes of an image and flips the y axis. |
|
1 |
syco |
Synonymous codon usage Gribskov statistic plot |
|
5 |
syndiva |
diversity analysis of synthetic libraries of a Fibronectin domain |
|
1 |
T Test for Two Samples |
|
|
2 |
T-Coffee |
multiple sequence alignment |
|
3 |
Table Compute |
computes operations on table data |
|
4 |
Table Merge |
Merging dataMatrix with a metadata table |
|
2 |
Table to GFF3 |
|
|
2 |
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 identifications validation |
Integrate identifications from animal detection on acoustic recordings |
|
1 |
Tag pileup frequency |
|
|
3 |
tar-to-directory |
converter |
|
2 |
TargetedFileConverter |
Converts different transition files for targeted proteomics / metabolomics analysis. |
|
4 |
TargetFinder |
plant small RNA target prediction tool |
Sequence alignment
|
2 |
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 |
tcode |
Fickett TESTCODE statistic to identify protein-coding DNA |
|
5 |
TEfinder |
Transposable element insertions finder |
|
2 |
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 to wordmatrix |
by extracting most frequent words |
|
1 |
Text transformation |
with sed |
|
11 |
TextExporter |
Exports various XML formats to a text file. |
|
4 |
textsearch |
Search sequence documentation. Slow, use SRS and Entrez! |
|
5 |
TGS-GapCloser |
fills the N-gap of error-prone long reads |
|
1 |
Thermo |
RAW file converter |
|
9 |
Thread nucleotides onto a protein alignment (back-translation) |
Gives a codon aware alignment |
|
5 |
TICCalculator |
Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). |
|
4 |
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 |
TOFCalibration |
Applies time of flight calibration. |
|
4 |
Tombo create |
browser text output |
|
1 |
Tombo detect modifications |
detecting shifts in raw current signal level, indicative of non-canonical bases |
|
1 |
Tombo plot genome locations |
Plotting amperage signal from nanopore reads at the locations specified |
|
1 |
Tombo plot most signficant |
Plotting amperage signal at the locations deemed most significant by the tombo |
|
1 |
Tombo Re-squiggle |
Raw Signal (electric current nanopore measurements) Genomic Alignment |
|
1 |
TopHat |
Gapped-read mapper for RNA-seq data |
|
9 |
Tophat Fusion Post |
post-processing to identify fusion genes |
|
2 |
TopPerc |
Facilitate input to Percolator and reintegrate. |
|
2 |
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 a CheRRI model using RRIs |
|
|
2 |
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 |
Transcript Integrity Number |
evaluates RNA integrity at a transcript level |
|
8 |
TransDecoder |
finds coding regions within transcripts |
|
7 |
transeq |
Translate nucleic acid sequences |
|
5 |
Transform |
real vector graphs to sparse vectors |
|
1 |
Transformation |
Transforms the dataMatrix intensity values |
|
1 |
TransformationEvaluation |
Applies a transformation to a range of values |
|
4 |
Translate BED Sequences |
3 frame translation of BED augmented with a sequence column |
|
1 |
Translate BED transcripts |
cDNA in 3frames or CDS |
|
1 |
Translate nucleotides |
to amino acids |
|
1 |
Transpose |
rows/columns in a tabular file |
|
5 |
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 |
TreeBeST best |
Generate a phylogenetic tree using CDS alignment and species tree |
|
1 |
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 putative adapter sequence |
|
|
1 |
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 |
Trinotate |
functional transcript annotation |
|
4 |
tRNA and tmRNA |
prediction (Aragorn) |
|
3 |
tRNA prediction |
(tRNAscan) |
|
2 |
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 |
UCSC Cell Browser |
displays single-cell clusterized data in an interactive web application. |
|
5 |
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 |
UNetCoreograph |
TMA core detection and dearraying |
|
1 |
Unfold |
columns from a table |
|
11 |
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 |
|
9 |
Unique |
occurrences of each record |
|
1 |
Unique lines |
assuming sorted input file |
|
11 |
Unique.seqs |
Return unique sequences |
|
5 |
Univariate |
Univariate statistics |
|
2 |
UnMicst |
Image segmentation - probability map generation |
|
1 |
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 |
Unzip |
Unzip file |
|
1 |
Upload File |
from your computer |
Query and retrieval
|
3 |
UpSet diagram |
of intersection of genomic regions or list sets |
|
4 |
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 ISO 19139 |
metadata documents |
|
1 |
ValidateSamFile |
assess validity of SAM/BAM dataset |
|
15 |
VAPOR |
Classify Influenza samples from short reads sequence data |
|
4 |
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 |
process variant counts |
|
3 |
Variant Frequency Plot |
Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data |
Aggregation
|
4 |
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 |
VCF to MAF Custom Track |
for display at UCSC |
|
2 |
VCF to pgSnp |
Convert from VCF to pgSnp format |
|
1 |
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 |
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 |
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 |
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 |
virhunter |
Deep learning method to identify viruses in sequencing datasets |
|
4 |
Visceral |
Evaluate Segmentation |
|
1 |
Visualisation |
of compounds |
|
5 |
Visualize |
the optimal scoring subnetwork |
|
2 |
Visualize with Krona |
Visualise any hierarchical data |
|
1 |
Vitessce Visualization |
integrative visualization of multi-modal, spatial single-cell 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 |
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 |
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 |
wordmatch |
Finds all exact matches of a given size between 2 sequences |
|
5 |
WTDBG |
De novo assembler AND consensuser for long noisy sequences |
|
3 |
X!Tandem MSMS Search |
Run an X!Tandem Search |
|
2 |
X!Tandem MSMS Search |
Run an X!Tandem Search - test |
|
1 |
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 |
XFDR |
Calculates false discovery rate estimates on crosslink identifications |
|
2 |
xmlstarlet |
convert a metadata XML file in one standard to another |
|
1 |
XMLValidator |
Validates XML files against an XSD schema. |
|
4 |
XPath |
compute xpath expressions on XML data |
|
2 |
XTandemAdapter |
Annotates MS/MS spectra using X! Tandem. |
|
5 |
xtc-to-dcd |
converter |
|
1 |
YAHS |
yet another HI-C scaffolding tool |
|
4 |
zerone |
|
|
1 |
zonal statistics |
over each area |
|
1 |