Examples : samtools, bed, topic:conversion

3397 tool(s) found

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