Examples : samtools, bed, topic:conversion

3081 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
'FeatureStein' fragment overlay scoring feature overlay scoring 1
2D Feature Extraction Feature Extraction 3
aaChanges amino-acid changes caused by a set of SNPs 2
ab1 to FASTQ converter 1
ABRicate Mass screening of contigs for antimicrobial and virulence genes Antimicrobial resistance prediction 9
ABRicate List List all of abricate's available databases. Antimicrobial resistance prediction 9
ABRicate Summary Combine ABRicate results into a simple matrix of gene presence/absence Antimicrobial resistance prediction 1
Abundance index computation across species, sites and years 1
ABySS de novo sequence assembler 9
AccurateMassSearch Match MS signals to molecules from a database by mass. 5
Adapt an elastic transformation to a new image size with bUnwarpJ 2
AdapterRemoval: remove adapter sequences from HTS data 1
Add column to an existing dataset Editing 2
Add hydrogen atoms at a certain pH value 6
Add input name as column to an existing tabular file 3
Add line to file writes a line of text at the begining or end of a text file. 1
Add LoFreq alignment quality scores to aligned read SAM/BAM records 4
Add or remove noise 2
Add or Replace Groups 3
Add shadow effect 2
add-read-counts Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file 2
AddCommentsToBam add comments to BAM dataset 14
Adding New Topology Information to a GROMACS topology file 1
AdditiveSeries Computes an additive series to quantify a peptide in a set of samples. 4
AddOrReplaceReadGroups add or replaces read group information 14
Adjust threshold of binary image 2
Admixture : Map genomic intervals resembling specified source populations 4
Advanced restitution: 'Point fixe' protocol from Animal Detection on Acoustic Recordings 1
Advanced restitution: 'Routier'or 'Pedestre' protocols from Animal Detection on Acoustic Recordings 1
AEGeAn GAEVAL compute coverage and integrity scores for gene models using transcript alignments. Genome annotation 1
AEGeAn LocusPocus calculate locus coordinates for the given gene annotation Genome annotation 1
AEGeAn ParsEval compare two sets of gene annotations for the same sequence. Genome annotation 1
Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster 1
Aggregate datapoints Appends the average, min, max of datapoints per interval 2
Aggregate Individuals : Append summary columns for a population 3
Alchemical Analysis Analysis of alchemical free energy calculations 1
ALDEx2 differential abundance analysis 1
Alevin Quantification and analysis of 3-prime tagged-end single-cell sequencing data 8
Align GraphClust cluster structural alignment and conservation analysis of predicted clusters 1
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 12
Align Samples - Align peaks across Peaklists 2
Align sequences to a reference using a codon alignment algorithm 6
Align sequences using a variety of alignment methods (align_seqs) 2
Align two images with bUnwarpJ 2
Align.check Calculate the number of potentially misaligned bases 6
Align.seqs Align sequences to a template alignment 5
alignmentsieve Filter BAM/CRAM files according to specified parameters 7
alimask append modelmask line to a multiple sequence alignments 7
Alleyoop - post-processing and QC of Slamdunk analyses 5
Alphafold 2 - AI-guided 3D structural prediction of proteins Protein structure prediction 8
Amova Analysis of molecular variance 5
AmpliCan analysis tool for genome editing 1
ampvis2 alpha diversity 1
ampvis2 boxplot 1
ampvis2 core community analysis 1
ampvis2 export fasta 1
ampvis2 frequency plot 1
ampvis2 heatmap 1
ampvis2 load 1
ampvis2 merge ampvis2 data sets 1
ampvis2 merge replicates 1
ampvis2 octave plot 1
ampvis2 ordination plot 1
ampvis2 OTU network plot 1
ampvis2 rank abundance plot 1
ampvis2 rarefaction curve 1
ampvis2 set metadata types 1
ampvis2 subset data by taxonomy 1
ampvis2 subset samples by sample metadata 1
ampvis2 timeseries plot 1
ampvis2 venn diagram 1
Analyze particles of binary image 2
Analyze skeleton 2
Analyze statistical significance of sample groupings using distance matrices (compare_categories) 2
Ancestry : Characterize ancestries w.r.t. inferred ancestral populations 2
ANCOM-BC differential abundance analysis 1
Angle Analysis - time series of Angles 5
Anisotropic Diffusion Edge-preserving, Anisotropic diffusion 2
AnnData Operations modifies metadata and flags genes 13
Annotate a VCF dataset with custom filters 1
Annotate a newick tree with HyPhy 6
Annotate opens an IFrame to Apollo 8
Annotate DESeq2/DEXSeq output tables Append annotation from GTF to differential expression tool outputs 2
Annotate RNAz 1
Annotate with DGI database info 1
Annotate with DGI database info 1
annotateMyIDs annotate a generic set of identifiers 11
annotatePeaks 4
Anosim Non-parametric multivariate analysis of changes in community structure 5
Anova N-way anova. With ou Without interactions 3
antaRNA Ant Colony Optimized RNA Sequence Design 1
AnteChamber - Amber's molecular input file processor 8
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 5
Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters 7
APoc Large-scale identification of similar protein pockets 2
Apply elastic transformation with bUnwarpJ 2
Apply raw transformation with bUnwarpJ 2
Arithmetic Operations on tables 2
Arriba detect gene fusions from STAR aligned RNA-Seq data 4
Arriba Draw Fusions 4
Arriba Get Filters to history 4
ARTIC guppyplex Filter Nanopore reads by read length and (optionally) quality 3
ARTIC minion Build consensus sequence and call variants from amplicon-based nanopore sequence data 5
ASCA Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block 1
ASHLAR Alignment by Simultaneous Harmonization of Layer/Adjacency Registration 1
AssayGeneratorMetabo Assay library generation from DDA data (Metabolomics) 3
Assemble with MIRA v3.4 Takes Sanger, Roche, Illumina, and Ion Torrent data 2
Assign taxonomy to each sequence (assign_taxonomy) 2
Associate HUMAnN2 functions with metadata 3
Association of points in consecutive frames (slices) using the nearest neighbor algorithm 3
Augustus gene prediction for prokaryotic and eukaryotic genomes 8
Auto Threshold applies a standard threshold algorithm to an image 3
Autocorrelation test check for temporal autocorrelation in the residuals 1
Automated multiple sequence alignment with pipelign 1
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
b2bTools: Biophysical predictors for single sequences from their amino-acid sequences 1
backtranseq Back translate a protein sequence 7
Bakta genome annotation via alignment-free sequence identification 2
BAM Coverage Plotter Plot read coverage across a genomic contig 1
BAM filter Removes reads from a BAM file based on criteria 4
BAM Index Statistics 3
BAM to Wiggle converts all types of RNA-seq data from .bam to .wig 10
bam-to-bai converter 1
BAM/SAM Mapping Stats reads mapping statistics for a provided BAM or SAM file. 10
bamCompare normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them 16
bamCoverage generates a coverage bigWig file from a given BAM or CRAM file 18
BamHash Hash BAM and FASTQ files to verify data integrity 1
BamLeftAlign indels in BAM datasets 12
bamPEFragmentSize Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files 16
BamUtil diff two coordinate sorted SAM/BAM files Sequence cutting 1
banana Bending and curvature plot in B-DNA 5
Bandage Image visualize de novo assembly graphs 8
Bandage Info determine statistics of de novo assembly graphs 6
bank_inhouse search by accurate mass (and by Retention time) on a local bank 1
Bar chart for multiple columns 2
Barcode Splitter 4
Barplot stratified HUMAnN features Nucleic acid sequence analysis Phylogenetic analysis 3
Barplot stratified HUMAnN2 features 3
barrnap Locate ribosomal RNA's in a fasta file. (GFF output) 4
Base Count 1
Base Coverage of all intervals Quantification 5
BaselineFilter Removes the baseline from profile spectra using a top-hat filter. 4
BaSiC Illumination ImageJ BaSiC shading correction for use with Ashlar 1
basil Breakpoint detection, including large insertions 1
Batch_correction Corrects intensities for signal drift and batch-effects 4
bax2bam converts PacBio basecall format (bax.h5) into BAM Conversion 2
BayeScan Detecting natural selection from population-based genetic data 1
BBTools: BBduk decontamination using kmers Global alignment Pairwise sequence alignment 3
BBTools: BBMap short-read aligner 4
BBTools: call variants in aligned Bam files 2
bcf_uncompressed-to-bcf converter 1
bcftools annotate Annotate and edit VCF/BCF files 11
bcftools call SNP/indel variant calling from VCF/BCF 12
bcftools cnv Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values 14
bcftools color-chrs plugin Color shared chromosomal segments, requires phased GTs 8
bcftools concat Concatenate or combine VCF/BCF files 10
bcftools consensus Create consensus sequence by applying VCF variants to a reference fasta file 13
bcftools convert from vcf Converts VCF/BCF to IMPUTE2/SHAPEIT formats 10
bcftools convert to vcf Converts other formats to VCF/BCFk 10
bcftools csq Haplotype aware consequence predictor 11
bcftools filter Apply fixed-threshold filters 10
bcftools frameshifts plugin Annotate frameshift indels 8
bcftools gtcheck Check sample identity 10
bcftools isec Create intersections, unions and complements of VCF files 11
bcftools merge Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file 11
bcftools mpileup Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files 11
bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows 13
bcftools query Extracts fields from VCF/BCF file and prints them in user-defined format 11
bcftools reheader Modify header of VCF/BCF files, change sample names 10
bcftools roh HMM model for detecting runs of homo/autozygosity 10
bcftools setGT plugin Sets genotypes 10
bcftools split-vep plugin Extracts fields from structured annotations such as INFO/CSQ 4
bcftools stats Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats 12
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 14
bcftoolsView Convert, filter, subset VCF/BCF files 1
Beagle phasing genotypes and imputing ungenotyped markers Haplotype mapping 1
BEAM significant single- and multi-locus SNP associations in case-control studies 1
bed to protein map genomic location of proteins for MVP 2
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BedCov calculate read depth for a set of genomic intervals 5
bedgraph-to-bigwig converter 1
BedToIntervalList convert coordinate data into picard interval list format 14
bedtools AnnotateBed annotate coverage of features from multiple files 21
bedtools BAM to BED converter 23
bedtools BED to BAM converter 21
bedtools BED to IGV create batch script for taking IGV screenshots 16
bedtools BED12 to BED6 converter 20
bedtools BEDPE to BAM converter 21
bedtools ClosestBed find the closest, potentially non-overlapping interval 21
bedtools ClusterBed cluster overlapping/nearby intervals 20
bedtools ComplementBed Extract intervals not represented by an interval file 21
bedtools ExpandBed replicate lines based on lists of values in columns 20
bedtools FisherBed calculate Fisher statistic between two feature files 20
bedtools FlankBed create new intervals from the flanks of existing intervals 21
bedtools Genome Coverage compute the coverage over an entire genome 20
bedtools GroupByBed group by common cols and summarize other cols 20
bedtools JaccardBed calculate the distribution of relative distances between two files 20
bedtools LinksBed create a HTML page of links to UCSC locations 20
bedtools MakeWindowsBed make interval windows across a genome 21
bedtools MaskFastaBed use intervals to mask sequences from a FASTA file 20
bedtools Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 20
bedtools MergeBED combine overlapping/nearby intervals into a single interval 20
bedtools MultiCovBed counts coverage from multiple BAMs at specific intervals 20
bedtools Multiple Intersect identifies common intervals among multiple interval files 23
bedtools OverlapBed computes the amount of overlap from two intervals 20
bedtools RandomBed generate random intervals in a genome 21
bedtools ReldistBed calculate the distribution of relative distances 20
bedtools ShuffleBed randomly redistrubute intervals in a genome 21
bedtools SlopBed adjust the size of intervals 22
bedtools SortBED order the intervals 20
bedtools SpacingBed reports the distances between features 17
bedtools SubtractBed remove intervals based on overlaps 20
bedtools TagBed tag BAM alignments based on overlaps with interval files 20
bedtools WindowBed find overlapping intervals within a window around an interval 20
Between-table Correlation Correlation table between two tables and graphic representation 2
bigwig-to-wig converter 1
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them 16
bigWigToBedGraph Convert from bigWig to bedGraph format 2
Bin.seqs Order Sequences by OTU 5
Binary 2 Label Converts Binary to Label Image 2
Binary To Points Converts Binary Image to Points 1
Binning refiner refines metagenome bins 2
Biom.info create shared and taxonomy files from biom 2
biom2-to-biom1 converter 1
Bionano Hybrid Scaffold automates the scaffolding process Genome assembly 7
biosed Replace or delete sequence sections 5
Biosigner Molecular signature discovery from omics data 2
biosyntheticSPAdes biosynthetic gene cluster assembly 6
BiSCoT Bionano scaffolding correction 1
Bismark bisulfite mapper (bowtie) 2
Bismark Deduplicate Deduplicates reads mapped by Bismark 9
Bismark Mapper Bisulfite reads mapper 15
Bismark Meth. Extractor Reports on methylation status of reads mapped by Bismark 11
Bismark Pretty Report Generates a graphical HTML report page from report outputs of Bismark 9
Blank Filter - Remove 'blank' peaks from the biological mass spectra 2
BLAST parser Convert 12- or 24-column BLAST output into 3-column hcluster_sg input 2
BLAST Reciprocal Best Hits (RBH) from two FASTA files 5
BLAST top hit descriptions Make a table from BLAST output 2
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 18
Blast2GO Maps BLAST results to GO annotation terms 3
BlastXML to gapped GFF3 1
BlobToolKit genome assembly QC 1
blockbuster detects blocks of overlapping reads using a gaussian-distribution approach 3
BlockClust efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles 2
Bowtie2 - map reads against reference genome 21
Boxplot of quality statistics 2
breseq find mutations in haploid microbial genomes DNA mapping Genetic mapping Genome annotation Mapping assembly Protein SNP mapping Sequence word comparison 4
btwisted Calculates the twisting in a B-DNA sequence 5
Build a UPGMA tree comparing samples (upgma_cluster) 2
Build base quality distribution 1
Build custom track for UCSC genome browser 3
Build Deep learning Batch Training Models with online data generator for Genomic/Protein sequences and images 5
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 12
Build tLEaP interactively build and run tLEaP files to set up systems with AmberTools 1
Busco assess genome assembly and annotation completeness 15
Butina Cluster using RDKit 2
Butina Cluster Matrix using RDKit 2
BWA-MEM2 - map medium and long reads (> 100 bp) against reference genome 1
bwameth Fast and accurate aligner of BS-Seq reads. 6
bwtool-lift Project data base-by-base into a new assembly using a liftOver chain file from UCSC 1
Cactus whole-genome multiple sequence alignment 7
Cactus: export whole-genome multiple sequence alignment to other formats 9
cai CAI codon adaptation index 5
cai custom CAI codon adaptation index using custom codon usage file 5
Calculate a Heinz score for each node 2
Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity) 2
Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables (beta_diversity) 2
Calculate community metrics calculate community metrics from abundance data 3
Calculate contig depths for MetaBAT2 3
Calculate metrics for classification performance 12
Calculate metrics for regression performance 11
Calculate molecular descriptors with Mordred 3
Calculate plane of best fit for molecules using RDKit 2
Calculate presence absence table calculate presence absence table from observation data 3
Calculate protein properties 2
Calculate sequence complexity total and per read 3
Calculate the box parameters using RDKit for an AutoDock Vina job from a ligand or pocket input file (confounding box) 5
Call and phase heterozygous SNPs 4
Call specific mutations in reads: Looks for reads with mutation at known positions and calculates frequencies and stats. 3
Call variants with LoFreq 7
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 9
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 9
Canonical Correlation Analysis 1
Canu assembler Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore 4
cap3 Sequence Assembly tool DNA mapping Mapping Mapping assembly Sequence assembly 2
cast expand combinations of variables:values to columnar format 1
CAT add_names annotate with taxonomic names 1
CAT bins annotate with taxonomic classification 2
CAT contigs annotate with taxonomic classification 2
CAT prepare a database for CAT - Contig Annotation Tool 1
CAT summarise the number of contigs or bins assigned to each taxonomic name 1
Categorize by collapsing hierarchical data to a specified functional level 2
Categorize Elements satisfying criteria 1
CCAT Control-based ChIP-seq Analysis Tool 2
cd-hit Cluster or compare biological sequence datasets 2
CDO get info Climate Data Information Operators to get information on Climate and NWP model data Calculation 1
CDO Operations Climate Data Manipulation Operators operations for standard processing of climate and NWP model output. Calculation 1
Cell types - build cell ontology map Create a mapping from labels to CL terms 3
Cell types - combine tools outputs Combine predictions for single tool from multiple datasets 4
Cell types - get consensus outputs across multiple tools 4
Cell types - get empirical distribution for tool performance table 3
Cell types - get tool p-values Get p-values for tool performance metrics 3
Cell types - get tool performance table Get performance table for a list of outputs generated by various tools 3
CellProfiler run a CellProfiler pipeline 1
CellProfiler run a CellProfiler pipeline 2
CEMiTool gene co-expression network analyses 1
CESM Community Earth System Model Ecological modelling Modelling and simulation 1
Change Case of selected columns 2
Change title to metadata value. 6
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 5
Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files 2
Check user's metadata mapping file for required data, valid format (validate_mapping_file) 2
CheckM analyze Identify marker genes in bins and calculate genome statistics 1
CheckM lineage_set Infer lineage-specific marker sets for each bin 1
CheckM lineage_wf Assessing the completeness and contamination of genome bins using lineage-specific marker sets 1
CheckM plot for assessing the quality of genome bins 1
CheckM qa Assess bins for contamination and completeness 1
CheckM taxon_set Generate taxonomic-specific marker set 1
CheckM taxonomy_wf Analyze all genome bins with the same marker set 1
CheckM tetra Calculate tetranucleotide signature of sequences 1
CheckM tree Place bins in the genome tree 1
CheckM tree_qa Assess phylogenetic markers in the genome tree 1
checktrans Reports STOP codons and ORF statistics of a protein 5
ChEMBL structure pipeline for curation and standardizing of molecular structures 2
chicAggregateStatistic computes with a target file the to be tested regions for chicDifferentialTest 7
chicDifferentialTest computes differential interactions of viewpoints 7
chicPlotViewpoint creates plots for viewpoints 7
chicQualityControl generates an estimate of the quality of each viewpoint 7
chicSignificantInteractions computes viewpoints with the given reference points and a background model 7
chicViewpoint computes viewpoints with the given reference points and a background model. 7
chicViewpointBackgroundModel compute a background model for cHi-C / HiChIP data 6
Chimera.bellerophon Find putative chimeras using bellerophon 5
Chimera.ccode Find putative chimeras using ccode 6
Chimera.check Find putative chimeras using chimeraCheck 5
Chimera.perseus Find putative chimeras using chimeraCheck 6
Chimera.pintail Find putative chimeras using pintail 5
Chimera.slayer Find putative chimeras using slayer 5
Chimera.uchime Find putative chimeras using uchime 5
Chimera.vsearch find potential chimeric sequences using vsearch 4
ChIPpeakAnno annoPeaks annotate peaks by annoGR object in the given range 1
chips Codon usage statistics 5
ChIPseeker for ChIP peak annotation and visualization 6
ChiRA collapse deduplicate fastq reads 17
ChiRA extract extrat the chimeras 17
ChiRA map map reads to trascriptome 17
ChiRA merge merge aligned positions 17
ChiRA qauntify quantify aligned loci to score the alignments 17
Chop.seqs Trim sequences to a specified length 6
Chromeister ultra-fast pairwise genome comparisons 5
cif2cell convert .cif file to .cell 2
CIRCexplorer 2
CIRCexplorer2 circular RNA analysis 1
Circos visualizes data in a circular layout Visualisation 11
Circos: Alignments to links reformats alignment files to prepare for Circos Parsing 10
Circos: bigWig to Scatter reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots Conversion 10
Circos: Bundle Links reduce numbers of links in datasets before plotting Aggregation 10
Circos: Interval to Circos Text Labels reformats interval files to prepare for Circos text labels Conversion 10
Circos: Interval to Tiles reformats interval files to prepare for Circos tile plots Conversion 10
Circos: Link Density Track reduce links to a density plot Aggregation 10
Circos: Resample 1/2D data reduce numbers of points in a dataset before plotting Aggregation 10
Circos: Stack bigWigs as Histogram reformats for use in Circos stacked histogram plots Formatting 6
Circos: Table viewer easily creates circos plots from tabular data Visualisation 10
cirdna Draws circular maps of DNA constructs 5
CITE-seq-Count Count CMO/HTO 1
Clair3 germline small variant caller for long-reads 2
Classify.otu Assign sequences to taxonomy 5
Classify.rf description 2
Classify.seqs Assign sequences to taxonomy 5
Classify.tree Get a consensus taxonomy for each node on a tree 5
CleanSam perform SAM/BAM grooming 14
Clearcut Generate a tree using relaxed neighbor joining 5
climate stripes from timeseries Visualisation 3
Clip adapter sequences 6
CLIP Peakcaller find CLIP peaks in blockbuster data 1
Clipping Profile estimates clipping profile of RNA-seq reads from BAM or SAM file 10
Close relatives : Discover familial relationships 2
Closed-reference OTU picking Shotgun UniFrac workflow (pick_closed_reference_otus) 2
ClustalW multiple sequence alignment program for DNA or proteins 5
Cluster the intervals of a dataset Sequence clustering Sequence merging 5
Cluster Assign sequences to OTUs (Operational Taxonomic Unit) 4
Cluster Inspection using RaceID examines gene expression within clusters 6
Cluster KEGG : Group gene categories connected by shared genes 2
Cluster ligands using SuCOS based on the overlap of 3D features 3
Cluster Profiler Bitr converting ID types 1
Cluster Profiler GO run GO Analysis 1
Cluster, infer trajectories and embed with scanpy 7
Cluster.classic Assign sequences to OTUs (Dotur implementation) 5
Cluster.fragments Group sequences that are part of a larger sequence 5
Cluster.split Assign sequences to OTUs and split large matrices 5
cluster_collection_report 4
Clustering using RaceID performs clustering, outlier detection, dimensional reduction 6
ClusterMassTraces Creates pseudo spectra. 2
ClusterMassTracesByPrecursor Correlate precursor masstraces with fragment ion masstraces in SWATH maps based on their elution profile. 2
cmalign Align sequences to a covariance model against a sequence database 3
cmbuild Build covariance models from sequence alignments 4
CMCV visualization of comparisons between RNA family models (CM) 1
cmfinder 3
cml-to-mol2 converter 1
cml-to-smi converter 2
cmpress Prepare a covariance model database for cmscan 2
cmscan Search sequences against collections of covariance models 2
cmsearch Search covariance model(s) against a sequence database 3
cmstat Summary statistics for covariance model 3
cmv CMV is a tool for visualization of RNA family models, also known as covariance models (CM) 2
codcmp Codon usage table comparison 5
codeML Detects positive selection (paml package) 3
coderet Extract CDS, mRNA and translations from feature tables 5
Codon count gives numbers of all different codons in the whole sequence 1
Cofold An RNA secondary structure prediction method that takes co-transcriptional folding into account 1
Cojac: mutbamscan scan an alignment file for mutation co-occurrences 1
Cojac: pubmut render a JSON or YAML file to a pretty table 1
Cojac: tabmut export cooccurrence mutations as a table 1
Collapse sequences 3
Collapse Collection into single dataset in order of the collection 5
Collapse samples Collapse samples in a BIOM table and mapping file 1
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 14
Collect.shared Generate collector's curves for calculators on OTUs 5
Collect.single Generate collector's curves for OTUs 6
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 14
CollectGcBiasMetrics charts the GC bias metrics 14
CollectHsMetrics compute metrics about datasets generated through hybrid-selection (e.g. exome) 4
CollectInsertSizeMetrics plots distribution of insert sizes 14
Collector’s curve of sequencing yield over time 2
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 15
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 14
Color Deconvolution Color deconvolution 2
ColorToGray converts color and channel-stacked images to grayscale 2
Column arrange by header name 2
Column Join on Collections 5
Column Regex Find And Replace 6
Combine FASTA and QUAL into FASTQ Aggregation 5
Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances 3
CometAdapter Annotates MS/MS spectra using Comet. 3
Compalignp Fractional identities between alignments 2
Compare multiple VCF datasets 1
Compare BIOM tables Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. 3
Compare diversity indicators with remote sensing data 1
Compare elastic and raw deformation by warping index with bUnwarpJ 2
Compare opposite elastic deformations by warping index with bUnwarpJ 2
Compare outputs of HUMAnN2 for several samples and extract similar and specific information 2
Compare two Datasets to find common or distinct rows Filtering 1
Compare two raw deformations by warping index with bUnwarpJ 2
Complement intervals of a dataset Sequence coordinate conversion 6
CompNovo Performs a de novo peptide identification using the CompNovo engine. 4
CompNovoCID Performs a de novo peptide identification using the CompNovo engine. 4
Compose a raw and an elastic transformation into a raw transformation with bUnwarpJ 2
Compose two elastic transformations into a raw transformation with bUnwarpJ 2
Compose two raw transformations into another raw transformation with bUnwarpJ 2
Compound conversion - interconvert between various chemistry and molecular modeling data files 6
Compound search - an advanced molecular search program using SMARTS 5
Compress file(s) 1
compseq Count composition of dimer/trimer/etc words in a sequence 5
Compute on rows 10
Compute a PCA raster from remote sensing data 1
Compute beta diversity distance matrices and generate PCoA plots (beta_diversity_through_plots) 2
Compute biodiversity indices from remote sensing data 1
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 21
Compute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly 10
Compute GLM on community data Compute a GLM of your choice on community data 2
Compute GLM on population data Compute a GLM of your choice on population data 2
Compute Motif Frequencies in indel flanking regions 2
Compute Motif Frequencies For All Motifs motif by motif 2
Compute physico-chemical properties for a set of molecules 5
Compute quality statistics for SOLiD data 1
Compute quality statistics 3
Compute sequence length 6
Compute spectral indices as NDVI from remote sensing data 1
computeGCBias Determine the GC bias of your sequenced reads 17
computeMatrix prepares data for plotting a heatmap or a profile of given regions 18
computeMatrixOperations Modify or combine the output of computeMatrix in a variety of ways. 11
Concatenate two BED files Aggregation 6
Concatenate FASTA alignment by species 3
Concatenate datasets tail-to-head Aggregation 1
Concatenate datasets tail-to-head (cat) 11
Concatenate images 2
Concatenate multiple datasets tail-to-head 4
CONCOCT for metagenome binning 4
CONCOCT: Cut up contigs in non-overlapping or overlapping parts of equal length 4
CONCOCT: Extract a fasta file for each cluster 4
CONCOCT: Generate the input coverage table for CONCOCT 4
CONCOCT: Merge cut clusters and assign concensus clusters for the original contigs 4
Conformer calculation for molecules (confab) with OpenBabel 3
Consensus.seqs Find a consensus sequence for each OTU or phylotype 6
ConsensusID Computes a consensus of peptide identifications of several identification engines. 6
ConsensusMapNormalizer Normalizes maps of one consensusXML file 5
Constrained conformer generation with RDKit 2
Construct Expression Set Object Create an ExpressionSet object from tabular and textual data 5
Control-FREEC detects copy-number changes and allelic imbalances 3
Convert delimiters to TAB 1
Convert SOLiD output to fastq 1
Convert sequences to graphs 1
Convert between BIOM table formats 9
Convert : CSV, FSTAT, Genepop or VCF to either gd_snp or gd_genotype 2
Convert a 10X BAM file to FASTQ 1
Convert Amber topology and coordinate files to GROMACS format using acpype 1
Convert BAM to FASTA multiple sequence alignment 5
Convert BAM to ScIdx 2
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert binary image to EDM (Euclidean Distance Map) 2
Convert DIMSpy-based HDF5 to tsv 2
Convert elastic transformation to raw with bUnwarpJ 2
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert from BAM to FastQ 13
Convert genome coordinates between assemblies and genomes 2
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert GFF3 to prot_table for TRANSIT 4
Convert gffCompare annotated GTF to BED for StringTie results 4
Convert Glimmer to GFF 1
Convert GTF to BED12 1
Convert image Convert image 2
Convert Kraken data to Galaxy taxonomy representation 3
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert OBO to OWL 1
Convert OBO to RDF 1
Convert Parameters to AMBER prmtop in preparation for MMGBSA/MMPBSA 7
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Convert SAM to interval 2
Convert to binary (black and white) 2
Convert VCF to MAF with vcf2maf 3
Convert XMFA to gapped GFF3 3
Convert, Merge, Randomize BAM datasets and perform other transformations 7
ConvertFastaToPrositCSV Create Prosit CSV Input From a Protein FASTA 3
ConvertLibraryToBlib Convert EncyclopeDIA Library to BLIB for Skyline 3
ConvertObjectsToImage convert the identified objects into an image 2
ConvertPrositCSVToLibrary Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library 3
Converts genome bins in fasta format to scaffolds-to-bin table 3
Converts GTF to Annotations file for Homer 1
CoNvex Gap-cost alignMents for Long Reads 2
Cooccurrence tests whether presence-absence patterns differ from chance 6
Coordinates of ROI 2
Copernicus Atmosphere Data Store for retrieving data from the Atmosphere Monitoring Service Data retrieval Format detection Formatting 1
Copernicus Climate Data Store for retrieveing climate data Data retrieval Format detection Formatting 1
Copernicus Essential Climate Variables for assessing climate variability Data retrieval Format detection Formatting 2
coronaSPAdes SARS-CoV-2 de novo genome assembler 6
Corr.axes correlation of data to axes 5
correctGCBias uses the output from computeGCBias to generate GC-corrected BAM/CRAM files 16
Correlation for numeric columns 1
Cosine Content - measure the cosine content of the PCA projection 4
Count occurrences of each record 2
Count Covariates on BAM files 1
Count GFF Features 2
Count Objects in labled images 1
Count sequences Count the sequences in a fasta file 2
Count the sequences in a fasta file (count_seqs) 2
Count.groups counts the number of sequences represented by a specific group or set of groups 5
Count.seqs (aka make.table) counts the number of sequences represented by the representative 5
Coverage of a set of intervals on second set of intervals Comparison Filtering 5
Coverage Distributions : Examine sequence coverage for SNPs 2
CoverM-CONTIG 1
CoverM-GENOME read coverage and relative abundance calculator focused on metagenomics applications 1
CPAT coding potential assessment 1
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 5
cram-to-bam converter 2
Create a BedGraph of genome coverage 3
Create a deep learning model architecture using Keras 6
Create a genus level gene families file 4
Create a histogram of genome coverage 3
Create a model to recommend tools using deep learning 5
Create a plot from GLM data as temporal trend 1
Create assemblies with Unicycler pipeline for bacterial genomes Genome assembly 10
Create binary barcodes from regular barcodes. 3
Create Decoy Database (reverse) Creates a decoy search database by adding reverse sequences to an existing database 1
Create deep learning model with an optimizer, loss function and fit parameters 6
Create Frankenstein ligand for docking active site definition 3
Create GROMACS index files using make_ndx 4
Create GROMACS position restraints files using genrestr 4
Create InterMine Interchange Dataset 1
Create nested list based on filenames and batch sizes 2
Create new image 2
Create or Update Organism will create the organism if it doesn't exist, and update otherwise 9
Create phyloseq object from dada2 sequence and taxonomy tables 1
Create single interval as a new dataset 1
Create text file with recurring lines 9
Create three-dimensional PCoA plots to be visualized with Emperor (make_emperor) 2
Create.database creates a database file from a list, repnames, repfasta and contaxonomy file 5
CRISPR Recognition Tool (CRT) 2
CRISPR Studio facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect 1
Cross-contamination Barcode Filter for use in plate-based barcoded analyses 3
CrossMap BAM Convert genome coordinates or annotation files between genome assemblies 5
CrossMap BED Convert genome coordinates or annotation files between genome assemblies 5
CrossMap GFF Convert genome coordinates or annotation files between genome assemblies 5
CrossMap region Convert genome coordinates or annotation files between genome assemblies 2
CrossMap VCF Convert genome coordinates or annotation files between genome assemblies 4
CrossMap Wig Convert genome coordinates or annotation files between genome assemblies 4
CruxAdapter Identifies MS/MS spectra using Crux. 2
CryptoGenotyper classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data. 1
csv-to-tabular converter 1
CTD analysis of chemicals, diseases, or genes 1
CTSM/FATES-EMERALD Functionally Assembled Terrestrial Ecosystem Simulator Ecological modelling Modelling and simulation 2
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 8
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 11
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
Cuffnorm Create normalized expression levels 7
Cuffquant Precompute gene expression levels 4
cummeRbund visualize Cuffdiff output 3
cURL send cURL POST requests 1
Curve Fitting to data points using (1st- or 2nd-degree) polynomial function 3
cusp Create a codon usage table 5
Customize the marker sequences and metadata from the MetaPhlAn database Nucleic acid sequence analysis Phylogenetic analysis 6
CustomProDB Generate protein FASTAs from exosome or transcriptome data 2
Cut columns from a table Filtering 2
Cut columns from a table (cut) 9
Cutadapt Remove adapter sequences from FASTQ/FASTA Sequence editing 22
cuteSV detects long-read-based SVs 1
cutseq Removes a specified section from a sequence 5
CVInspector A tool for visualization and validation of PSI mapping and CV files. 6
dada2: assignTaxonomy and addSpecies Learn Error rates 6
dada2: dada Remove sequencing errors 6
dada2: filterAndTrim Filter and trim short read data 6
dada2: learnErrors Learn Error rates 6
dada2: makeSequenceTable construct a sequence table (analogous to OTU table) 6
dada2: mergePairs Merge denoised forward and reverse reads 6
dada2: plotComplexity Plot sequence complexity profile 6
dada2: plotQualityProfile plot a visual summary of the quality scores 6
dada2: removeBimeraDenovo Remove bimeras from collections of unique sequences 6
dada2: sequence counts 6
dan Calculates DNA RNA/DNA melting temperature 5
DAS Tool for genome resolved metagenomics 3
Data Fetch Query and retrieval 1
DatabaseFilter Filters a protein database (FASTA format) based on identified proteins 5
Datamash (operations on tabular data) 5
DAVID functional annotation for a list of genes 1
DBKit Create database 1
DBKit Extract entries 1
DBKit Merge two databases 1
dbnsfp.tabular-to-snpsiftdbnsfp converter 3
DCCM analysis - Dynamical Cross-Correlation Maps using Bio3D (DCCM) 2
DCS mutations to SSCS stats: Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies 3
DCS mutations to tags/reads: Extracts all tags that carry a mutation in the duplex consensus sequence (DCS) 3
dcTMD friction correction for calculating friction and free energy profiles from TMD ensembles 2
Decharger Decharges and merges different feature charge variants of the same peptide. 5
decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies 1
DecoyDatabase Create decoy sequence database from forward sequence database. 5
Deep learning training and evaluation conduct deep training and evaluation either implicitly or explicitly 4
DeepVariant deep learning-based variant caller Variant calling 3
Degap.seqs Remove gap characters from sequences 5
degapseq Removes gap characters from sequences 5
Delete all annotations from an Apollo record 8
Delete an Apollo record 8
Delete Overlapping Indels from a chromosome indels file 1
Deletion Profile calculates the distributions of deleted nucleotides across reads 6
Delly call and genotype structural variants 5
Delly classify somatic or germline copy-number variants 3
Delly cnv discover and genotype copy-number variants 3
Delly filter somatic or germline structural variants 5
Delly long-read (lr) optimized calling and genotyping of structural variants 6
Delly merge structural variants across/within BCF/VCF file(s) 5
Delta-Filter Filters alignment (delta) file from nucmer Read mapping Sequence alignment 5
DeMeanderize Orders the spectra of MALDI spotting plates correctly. 4
Describe samples and replicates 11
Descriptors calculated with RDKit 4
descseq Alter the name or description of a sequence 5
DESeq2 Determines differentially expressed features from count tables Differential gene expression profiling RNA-Seq quantification 22
detect CRISPR sequences (minced) 1
Detection Visualization Detection Visualization 3
Determine distance to defined points - determine the minimum distances between a molecule and a set of 3D points 2
Determine_batch_correction to choose between linear, lowess and loess methods 4
Deunique.seqs Return all sequences 5
Deunique.tree Reinsert the redundant sequence identiers back into a unique tree. 5
DEWSeq - A sliding window based peak caller for eCLIP/iCLIP data 1
DEXSeq Determines differential exon usage from count tables 10
DEXSeq-Count Prepare and count exon abundancies from RNA-seq data 10
DIA_Umpire_SE DIA signal extraction 1
DIAlignR for retention time alignment of targeted mass spectrometric data 1
Diamond alignment tool for short sequences against a protein database Sequence alignment analysis 9
Diamond makedb Build database from a FASTA file Sequence alignment analysis 8
Diamond view generate formatted output from DAA files Sequence alignment analysis 6
diapysef library generation generates spectral library for DIA analysis 1
diff analyzes two files and generates an unidiff text file with information about the differences and an optional Html report 3
Diffacto Comparative Protein Abundance from Covariation of Peptide Abundances 1
DiffBind differential binding analysis of ChIP-Seq peak data 12
Differential Cleavage : Select SNPs differentially cut by specified restriction enzymes 2
Differential expression analysis using a Trinity assembly 11
diffseq Find differences between nearly identical sequences 5
digest Protein proteolytic enzyme or reagent cleavage digest 5
Digestor Digests a protein database in-silico. 4
DigestorMotif digests a protein database in-silico 4
Dihedral Analysis Time series of dihedrals 5
DISCO to assemble metagenomics data using an overlap-layout-consensus (OLC) approach 2
Discriminant Analysis 12
DisplayDataOnImage produce an image with data on top of identified objects 2
Dist.seqs calculate uncorrected pairwise distances between aligned sequences 5
Dist.shared Generate a phylip-formatted dissimilarity distance matrix among multiple groups 5
Distance Analysis - time series using MDAnalysis 5
Diversity : pi, allowing for unsequenced intervals 2
DNAdiff Evaluate similarities/differences between two sequences Read mapping Sequence alignment 5
DotKnot pseudoknot prediction in a given RNA sequence 1
dotmatcher Displays a thresholded dotplot of two sequences 5
dotpath Non-overlapping wordmatch dotplot of two sequences 5
dottup Displays a wordmatch dotplot of two sequences 5
Download and Extract Reads in BAM format from NCBI SRA Data retrieval Formatting 24
Download and Generate Pileup Format from NCBI SRA 9
Download run data from EBI Metagenomics database 1
downloads via lftps 1
Downsample SAM/BAM Downsample a file to retain a subset of the reads 14
dpocket to calculate descriptors for protein pockets 1
Dr. Disco (bam-extract) Extracts reads from two targeted regions 1
Dr. Disco (classify) Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists 1
Dr. Disco (detect) Detects break-points in RNA-seq 1
Dr. Disco (fix) Fixes chimeric alignments from STAR 1
Dr. Disco (integrate) Merges corresponding genomic breaks and exon-to-exon junctions 1
DRAM annotate metagenome-assembled-genomes (MAGs) 1
DRAM distill metagenome-assembled-genomes (MAGs) 1
DRAM find neighborhoods around genes of interest 1
DRAM merge multiple annotations into a single set 1
DRAM strain annotations down to genes of interest 1
Draw nucleotides distribution chart 4
Draw phylogeny 1
Draw quality score boxplot for SOLiD data 1
Draw quality score boxplot 4
Draw ROC plot on "Perform LDA" output 2
Draw Stacked Bar Plots for different categories and different criteria 1
Draw variants : show positions of SNVs and unsequenced intervals 2
dreg Regular expression search of a nucleotide sequence 6
DREME - Discriminative Regular Expression Motif Elicitation 4
dRep compare compare a list of genomes 3
dRep dereplicate De-replicate a list of genomes 3
Droplet barcode rank plot Creates a barcode rank plot for quality control of droplet single-cell RNA-seq data 3
DropletUtils Utilities for handling droplet-based single-cell RNA-seq data DNA barcoding Parsing 9
DropletUtils emptyDrops Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment. 2
DropletUtils Read10x into SingleCellExperiment object 3
Drug-likeness quantitative estimation (QED) with RDKit 4
DTAExtractor Extracts spectra of an MS run file to several files in DTA format. 5
EBI SCXA Data Retrieval Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA) 2
EBI Search to obtain search results on resources and services hosted at the EBI 2
ectyper ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. 1
Edena (assembling) 1
Edena (overlapping) 1
edgeR Perform differential expression of count data Differential gene expression profiling RNA-seq read count analysis 10
edta Whole-genome de-novo TE annotation 1
EGA Download Client 5
eggNOG Mapper functional sequence annotation by orthology 10
EGSEA easy and efficient ensemble gene set testing 4
EICExtractor Extracts intensities from dedicates positions in a LC/MS map 5
einverted Finds DNA inverted repeats 5
ENA Upload tool 9
EncyclopeDIA Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data 3
EncyclopeDIA Quantify samples from Data-Independent Acquisition (DIA) MS/MS Data 3
End-to-End Analysis - End-to-End distance timeseries and histogram for the given selections 2
Enhance contrast 2
EnhanceOrSuppressFeatures to improve subsequent identification of objects 2
Ensemble methods for classification and regression 12
Enumerate changes calculated with Dimorphite DL and RDKit 2
EODIE converts simple features data between file formats 1
epestfind Finds PEST motifs as potential proteolytic cleavage sites 5
EpiCSeg - Chromatin segmentation 1
Epifany Runs a Bayesian protein inference. 2
equicktandem Finds tandem repeats 5
ERPairFinder Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans. 4
est2genome Align EST and genomic DNA sequences 5
Estimate Abundance at Taxonomic Level Bayesian Reestimation of Abundance with KrakEN Statistical calculation 3
Estimate Library Complexity 3
Estimate temporal population evolution by species 2
Estimate temporal population variation by specialization group 3
estimate-energy Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place 2
EstimateLibraryComplexity assess sequence library complexity from read sequences 14
estimateReadFiltering estimates the number of reads that would be filtered given certain criteria 6
Estimator attributes get important attributes from an estimator or scikit object 9
etandem Looks for tandem repeats in a nucleotide sequence 5
ETE GeneTree splitter from a genetree using the ETE Toolkit 7
ETE lineage generator from a list of species/taxids using the ETE Toolkit 5
ETE mod manipulates tree topology by rooting, pruning or sorting branches 4
ETE species tree generator from a list of species using the ETE Toolkit 4
ETE taxa DB generator generates the ETE sqlite DB from the NCBI taxdump.tar.gz 4
Evaluate a Fitted Model using a new batch of labeled data 6
Evaluate pairwise distances or compute affinity or kernel for sets of samples 12
Evaluation of RRIs using CheRRI 1
ExomeDepth Calls copy number variants (CNVs) from targeted sequence data 1
Exonerate pairwise sequence comparison 4
Expected temporal trend of species abundance 1
Export AnnData and loom files Interconvert AnnData and Loom formats 10
Export datasets to remote files source 1
Export to GraPhlAn 2
ExportToSpreadsheet export measurements into one or more files 2
eXpress Quantify the abundances of a set of target sequences from sampled subsequences 2
ExternalCalibration Applies an external mass recalibration. 6
Extract alignment ends from SAM or BAM 3
Extract and cluster differentially expressed transcripts from a Trinity assembly 12
Extract barcodes according to pattern 3
Extract clusters of MD trajectories from linkage matrix data 3
Extract CuffDiff tabular files from a cummeRbund database 2
Extract element identifiers of a list collection 2
Extract energy components with GROMACS 7
Extract FASTQ in tabular format from a set of FAST5 files 2
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Extract MAF blocks given a set of genomic intervals 4
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract nanopore events from a set of sequencing reads 2
Extract Pairwise MAF blocks given a set of genomic intervals 1
Extract reads in FASTA or FASTQ format from nanopore files 2
Extract RMSD distance matrix data from MD ensemble with MDAnalysis 3
Extract sequences from GenBank files (CDS, gene ...) 1
Extract the marker sequences and metadata from the MetaPhlAn database Nucleic acid sequence analysis Phylogenetic analysis 6
Extract time and channel information from a set of FAST5 files 2
Extract top view from whole-slice image 2
Extract values from an SD-file into a tabular file using RDKit 4
extract-boxed-sequences Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility 2
extractfeat Extract features from a sequence 5
Extracting Topology Information from a GROMACS topology file 1
extractseq Extract regions from a sequence 5
FalseDiscoveryRate Estimates the false discovery rate on peptide and protein level using decoy searches. 7
fargene Fragmented antibiotic resistance gene identifier 2
faSplit Split a FASTA file 3
FASTA header converter to append species information 1
FASTA Merge Files and Filter Unique Sequences Concatenate FASTA database files together 4
Fasta nucleotide color plot 2
Fasta nucleotide color plot 1
Fasta regular expression finder Search in fasta for regexp match 1
Fasta Statistics Display summary statistics for a fasta file. 5
FASTA Width formatter 3
fasta-to-fai converter 1
FASTA-to-Tabular converter 3
fasta_to_gspan 3
FastaCLI Appends decoy sequences to FASTA files 6
FastANI fast alignment-free computation of whole-genome Average Nucleotide Identity 1
Faster Download and Extract Reads in FASTQ format from NCBI SRA Data retrieval Formatting 15
FASTG2Protlib-Peptides Generate FASTA from FASTG 1
FASTG2Protlib-Validate Validate a candidate protein library 1
fastp - fast all-in-one preprocessing for FASTQ files 8
fastpca - dimensionality reduction of MD simulations 2
FASTQ de-interlacer on paired end reads Splitting 5
FASTQ Groomer convert between various FASTQ quality formats Sequence conversion 5
FASTQ info validates single or paired fastq files Format validation 1
FASTQ interlacer on paired end reads Aggregation 6
FASTQ joiner on paired end reads Aggregation 7
FASTQ Masker by quality score Sequence masking 5
FASTQ Quality Trimmer by sliding window 5
FASTQ splitter on joined paired end reads Splitting 6
FASTQ Summary Statistics by column Sequence assembly validation 4
FASTQ to FASTA converter Conversion 5
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 6
FASTQ to Tabular converter Sequence conversion 5
FASTQ Trimmer by column Sequence trimming 5
fastq-join - Joins two paired-end reads on the overlapping ends 3
Fastq.info Convert fastq to fasta and quality 6
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 18
FASTQE visualize fastq files with emoji's 🧬😎 5
fastqillumina-to-fqtoc converter 1
FastqToSam convert Fastq data into unaligned BAM 19
FASTTREE build maximum-likelihood phylogenetic trees Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
faToVcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs 1
Feature coverage 1
Feature Selection module, including univariate filter selection methods and recursive feature elimination algorithm 12
featureCounts Measure gene expression in RNA-Seq experiments from SAM or BAM files. Sequence assembly 25
FeatureFinderCentroided Detects two-dimensional features in LC-MS data. 5
FeatureFinderIdentification Detects features in MS1 data based on peptide identifications. 5
FeatureFinderIsotopeWavelet Detects two-dimensional features in LC-MS data. 5
FeatureFinderMetabo Assembles metabolite features from centroided (LC-)MS data using the mass trace approach. 5
FeatureFinderMetaboIdent Detects features in MS1 data based on metabolite identifications. 2
FeatureFinderMRM Detects two-dimensional features in LC-MS data. 4
FeatureFinderMultiplex Determination of peak ratios in LC-MS data 7
FeatureFinderSuperHirn Finds mass spectrometric features in mass spectra. 5
FeatureLinkerLabeled Groups corresponding isotope-labeled features in a feature map. 5
FeatureLinkerUnlabeled Groups corresponding features from multiple maps. 5
FeatureLinkerUnlabeledKD Groups corresponding features from multiple maps. 4
FeatureLinkerUnlabeledQT Groups corresponding features from multiple maps. 4
FEELnc FlExible Extraction of LncRNA 6
Fetch closest non-overlapping feature for every interval Filtering 4
Fetch Indels from 3-way alignments 1
Fetch taxonomic representation 2
FFEval Evaluation tool for feature detection algorithms. 4
fgsea - fast preranked gene set enrichment analysis 3
FidoAdapter Runs the protein inference engine Fido. 6
FileConverter Converts between different MS file formats. 5
FileFilter Extracts or manipulates portions of data from peak, feature or consensus-feature files. 5
FileInfo Shows basic information about the file, such as data ranges and file type. 5
FileMerger Merges several MS files into one file. 5
Filter data on any column using simple expressions Formatting 2
Filter with scanpy 7
Filter a set of molecules from a file 6
Filter a VCF file 1
Filter and merge chimeric reads from Arima Genomics 1
Filter BAM datasets on a variety of attributes 6
Filter BED on splice junctions that are not in a reference bed file 1
Filter by quality Filtering 6
Filter Combined Transcripts using tracking file 1
Filter FASTA on the headers and/or the sequences 5
Filter fasta to remove sequences based on input criteria (filter_fasta) 2
Filter FASTQ reads by quality score and length Filtering 4
Filter GFF data by attribute using simple expressions 2
Filter GFF data by feature count using simple expressions 1
Filter GTF data by attribute values_list 2
Filter Image applies a standard filter to an image 2
Filter low expression transcripts from a Trinity assembly 11
Filter MAF by specified attributes 1
Filter MAF blocks by Species 1
Filter MAF blocks by Size 1
Filter OTUs from an OTU table based on their observation counts or identifier (filter_otus_from_otu_table) 2
Filter pileup on coverage and SNPs 3
Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region 6
Filter segmentation Filter segmentation by rules 1
Filter sequence alignment by removing highly variable regions (filter_alignment) 2
Filter sequences by ID from a tabular file 5
Filter sequences by length Filtering 6
Filter sequences by mapping from SAM/BAM file 4
Filter SNPs : Discard some SNPs based on coverage, quality or spacing 4
Filter species with rare and low abundances 2
Filter Tabular 5
Filter taxa from an OTU table (filter_taxa_from_otu_table) 2
Filter with SortMeRNA of ribosomal RNAs in metatranscriptomic data 6
filter-annotated-entries Split entries into two files based on whether they overlap annotations in a bed file 2
filter-by-energy Split entries over two files based on the estimated energy 2
Filter.seqs removes columns from alignments 5
Filter.shared remove OTUs based on various critieria 6
Filters samples from an OTU table on the basis of the number of observations in that sample, or on the basis of sample metadata (filter_samples_from_otu_table) 2
FilterSamReads include or exclude aligned and unaligned reads and read lists 14
filtlong Filtering long reads by quality 3
FIMO - Scan a set of sequences for motifs 12
Find diagnostic hits 1
Find edges 2
find in reference filter peptides that are present in proteins 4
Find lowest diagnostic rank 1
Find maxima 2
find-boxes Finds all occurances of two given boxes (sequence motifs) within a FASTA file 2
findMotifsGenome 3
Finds SNP sites from a multi-FASTA alignment file 1
Fit a BUM model with p-values 2
Fit a Pipeline, Ensemble or other models using a labeled dataset 6
fix-fasta-headers Replaces all spaces with underscores in the ">.."-sequence headers of a FASTA file 2
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 14
FlaiMapper detects small ncRNA derived fragments in small RNA-Seq data 1
FLAIR collapse defines high-confidence isoforms from flair-corrected reads 3
FLAIR correct corrects misaligned splice sites using genome annotations 2
Flanking Sequence : Fetch DNA sequence for intervals surrounding the given SNPs 2
FLASH adjust length of short reads 7
FlashLFQ ultrafast label-free quantification for mass-spectrometry proteomics 5
Flight curve compute the regional expected pattern of abundance 1
Flye de novo assembler for single molecule sequencing reads Genome assembly 8
footprint 1
Format tree and trait tables 2
Format cd-hit outputs to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file 2
Format Fastq sequences and barcode data (extract_barcodes) 2
Format MetaPhlAn2 output to extract abundance at different taxonomic levels 2
Format MetaPhlAn2 output for Krona 2
Founders sequenced : Offspring estimated heterozygosity from a pedigree with sequenced founders 2
FPKM Count calculates raw read count, FPM, and FPKM for each gene 8
fpocket - find potential binding sites in protein structures 4
FragGeneScan for finding (fragmented) genes in short reads 2
Fragmenter splits a molecule in fragments 1
freak Residue/base frequency table or plot 5
FreeBayes bayesian genetic variant detector 12
Freyja: Aggregate and visualize demixed results 1
Freyja: Bootstrapping method 1
Freyja: Call variants and get sequencing depth information 1
Freyja: Demix lineage abundances 1
FuMa match detected fusion genes based on gene names (in particular for RNA-Seq) 1
Funannotate assembly clean 5
Funannotate compare annotations 5
Funannotate functional annotation 5
Funannotate predict annotation 6
FunDO human genes associated with disease terms 2
fuzznuc Nucleic acid pattern search 6
fuzzpro Protein pattern search 5
fuzztran Protein pattern search after translation 5
FuzzyDiff Compares two files, tolerating numeric differences. 4
g:Profiler tools for functional profiling of gene lists 1
Garnett - check markers Check marker file to filter out markers of suboptimal quality 1
Garnett - classify cells Classify cells into cell types 1
Garnett - get feature genes Obtain a list of genes used as features in classification model 1
Garnett - get standard output Get final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package 1
Garnett - train classifier Train classifier based on marker gene list 1
Garnett - transform markes Transform marker files from Single Cell Expression Atlas format to that compatible with Garnett 1
Garnett - update markers Update marker file by filtering out suboptimal markers 1
garnier Predicts protein secondary structure 5
Gate Finder displays a series of gating outcomes using Vitessce 1
GATK4 Mutect2 - Call somatic SNVs and indels via local assembly of haplotypes 8
GC Skew calculates skew over genomic sequences Nucleic acid property calculation 10
gd_snp to VCF : Convert from gd_snp or gd_genotype to VCF format, for submission to dbSNP 2
GDAL addo builds or rebuilds overview images 2
GDAL Build VRT builds a VRT from a list of datasets 2
GDAL Informations lists information about a raster dataset 2
GDAL Merge mosaics a set of images 2
GDAL Translate converts raster data between different formats. 2
GDAL Warp image reprojection and warping utility 2
GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs). Nucleic acid feature detection 3
Gecko Ungapped genome comparison 3
geecee Calculates fractional GC content of nucleic acid sequences 5
GEMINI actionable_mutations Retrieve genes with actionable somatic mutations via COSMIC and DGIdb 4
GEMINI amend Amend an already loaded GEMINI database. 5
GEMINI annotate the variants in an existing GEMINI database with additional information 7
GEMINI burden perform sample-wise gene-level burden calculations 4
GEMINI database info Retrieve information about tables, columns and annotation data stored in a GEMINI database 4
GEMINI fusions Identify somatic fusion genes from a GEMINI database 5
GEMINI gene_wise Custom genotype filtering by gene 5
GEMINI inheritance pattern based identification of candidate genes 2
GEMINI interactions Find genes among variants that are interacting partners 4
GEMINI load Loading a VCF file into GEMINI 7
GEMINI lof_sieve Filter LoF variants by transcript position and type 4
GEMINI pathways Map genes and variants to KEGG pathways 5
GEMINI qc Quality control tool 5
GEMINI query Querying the GEMINI database 5
GEMINI roh Identifying runs of homozygosity 5
GEMINI set_somatic Tag somatic mutations in a GEMINI database 5
GEMINI stats Compute useful variant statistics 4
GEMINI windower Conducting analyses on genome "windows" 4
GenBank and EBML to GFF converter 1
Genbank to GFF3 converter 2
genbank-to-genbank.gz converter 1
genbank.gz-to-genbank converter 1
Gene Align and Family Aggregator generates an SQLite database that can be visualised with Aequatus 2
Gene BED To Exon/Intron/Codon BED expander 1
Gene Body Coverage (BAM) Read coverage over gene body. 13
Gene Body Coverage (Bigwig) Read coverage over gene body 12
Gene Copy Number Finder from a genetree using the ETE Toolkit 2
Gene length and GC content from GTF and FASTA file 4
Generalized linear models for classification and regression 11
Generate random samples with controlled size and complexity 12
Generate A Matrix for using PC and LDA 1
Generate box-whisker plot of quality score distribution over positions in nanopore reads 2
Generate conformers using RDKit 2
Generate gene to transcript map for Trinity assembly 10
Generate heatmap with hierarchical clustering of both samplesand microbial clades for MetaPhlAn2 2
Generate histogram of nanopore read lengths 2
Generate MD topologies for small molecules using acpype 9
Generate pileup from BAM dataset 3
Generate SuperTranscripts from a Trinity assembly 6
Generation, personalization and annotation of tree for GraPhlAn 2
Generic_Filter Removes elements according to numerical or qualitative values 3
GeneSeqToFamily preparation converts data for the workflow 4
genform Generation of molecular formulas by high-resolution MS and MS/MS data 1
Genome annotation statistics 1
GenomeScope reference-free genome profiling 3
GenomicSuperSignature interpretation of RNAseq experiments 1
Genrich Detecting sites of genomic enrichment 3
Get all term synonyms of a given OBO term 1
Get all terms of a given OBO term 1
Get all the relationship IDs and definitions from the given OBO ontology 2
Get all the relationship IDs and names from the given OBO ontology 2
Get all the relationship IDs and namespaces from the given OBO ontology 1
Get all the relationship types from the given OBO ontology 2
Get all the term IDs and term names of a given OBO ontology 1
Get child terms of a given OBO term 1
Get crosslinked nucleotides from full alignments 3
Get features by Ensembl ID using REST API 3
Get flanks returns flanking region/s for every gene Sequence analysis 4
Get gene tree by Ensembl ID using REST API 4
Get homopolymer run length Annotate indel variants with homopolymer context 1
Get longest read from a set of FAST5 files. 2
Get Microbial Data Query and retrieval 1
Get motifs from AREsite2 AREsite2 REST Interface 1
Get organelle from reads 1
Get Pathways : Look up KEGG pathways for given Ensembl transcripts 2
Get PDB file from Protein Data Bank 2
Get peaklists or an average peaklist from a Peak Intensity Matrix 2
Get PubMed abstracts by PMID IDs 1
Get RT Stop Counts derives the reverse transcriptase (RT) stop count on each nucleotide from a mapped file provided by the Iterative Mapping module 1
Get sequences by Ensembl ID using REST API 3
Get species occurrences data from GBIF, ALA, iNAT and others 1
Get subontology from a given OBO term 1
Get the ancestor terms of a given OBO term Collects the ancestor terms from a given term in the given OBO ontology 2
Get the descendent terms of a given OBO term 1
Get the parent terms of a given OBO term 1
Get the root terms of a given OBO term 1
Get the terms filtered by a relationship type 1
Get the terms that are related by a concrete relationship type 2
Get.communitytype description 5
Get.coremicrobiome fraction of OTUs for samples or abundances 6
Get.dists selects distances from a phylip or column file 5
Get.group group names from shared or from list and group 6
Get.groups Select groups 5
Get.label label names from list, sabund, or rabund file 5
Get.lineage Picks by taxon 6
Get.mimarkspackage creates a mimarks package form with your groups 5
Get.otulabels Selects OTU labels 6
Get.otulist Get otus for each distance in a otu list 5
Get.oturep Generate a fasta with a representative sequence for each OTU 5
Get.otus Get otus containing sequences from specified groups 5
Get.rabund Get rabund from a otu list or sabund 6
Get.relabund Calculate the relative abundance of each otu 5
Get.sabund Get sabund from a otu list or rabund 5
Get.seqs Picks sequences by name 5
Get.sharedseqs Get shared sequences at each distance from list and group 5
GetFastaBed use intervals to extract sequences from a FASTA file 20
getorf Finds and extracts open reading frames (ORFs) 5
GFA to FASTA Convert Graphical Fragment Assembly files to FASTA format 4
gfastats the swiss army knife for genome assembly 8
GFF converter to GenBank or embl 1
GFF-to-BED converter Conversion 1
GFF3 to Apollo Annotations 8
gff3.bz2-to-gff3 converter 1
GffCompare compare assembled transcripts to a reference annotation 5
gffread Filters and/or converts GFF3/GTF2 records 7
GLASSgo sRNA homolog finder 2
Glimmer ICM builder 1
Glimmer3 Predict ORFs in prokaryotic genomes (knowlegde-based) 1
Glimmer3 Predict ORFs in prokaryotic genomes (not knowlegde-based) 1
GMAJ Multiple Alignment Viewer 1
GNPSExport Tool to export consensus features into MGF format 2
GOEnrichment performs GO enrichment analysis of a set of gene products 2
Golm Metabolome Database search spectrum : GC-MS Mass Spectral Database. 2
goseq tests for overrepresented gene categories Gene-set enrichment analysis 12
GOSlimmer converts a set of annotation from GO to a given GOSlim version 2
GotohScan Find subsequences in db 2
GPASS significant single-SNP associations in case-control studies 1
gProfiler Convert converts between various types of namespaces 2
gProfiler GOSt performs functional enrichment analysis of gene lists Gene-set enrichment analysis 2
gProfiler Orth translates gene identifiers between organisms 2
gProfiler Random generates a gene list 2
gProfiler SNPense maps SNP rs-codes to gene names, chromosomal coordinates and variant effects 2
Graphclust glob_report collect clusters 1
GraphEmbed Compute and plot a 2D embedding of a data matrix given supervised class information 1
GraPhlAn to produce graphical output of an input tree 2
GraphProt - Train models and predict RBP binding profiles 3
GrayToColor take grayscale images and produces a color image from them 2
gro-to-pdb converter 1
GROMACS check to provide information about GROMACS input files 2
GROMACS copy file from built-in datasets 2
GROMACS energy minimization of the system prior to equilibration and production MD 7
GROMACS initial setup of topology and GRO structure file 6
GROMACS production simulation for data collection 2
GROMACS Radius of Gyration of a molecular structure 2
GROMACS RMSD calculation of molecular structures 1
GROMACS RMSF calculation of molecular structures 1
GROMACS simulation for system equilibration or data collection 9
GROMACS solvation and adding ions to structure and topology files 8
GROMACS structure configuration using editconf 5
Group data by a column and perform aggregate operation on other columns. 4
Group abundances of UniRef50 gene families obtained (HUMAnN2 output) to Gene Ontology (GO) slim terms 2
GTF-to-BEDGraph converter Conversion 1
gtf-to-interval_index converter 1
GTF2GeneList extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer 6
Gubbins Recombination detection in Bacteria 2
Gumbel - determine essential genes 6
Hammock - cluster peptides Clusters short peptide sequences 5
hamronize parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 3
hamronize: summarize harmorization reports 4
Hapo-G genome polishing 1
Hardklor identification of features from mass spectra 4
Hcluster Assign sequences to OTUs (Operational Taxonomic Unit) 2
hcluster_sg Hierarchically clustering on a sparse graph 2
hcluster_sg parser converts hcluster_sg 3-column output into lists of IDs 4
HE/ MALDI Image Registration Registration of MALDI and HE Image 1
Heatmap Heatmap of the dataMatrix 2
Heatmap w ggplot 6
Heatmap.bin Generate a heatmap for OTUs 5
Heatmap.sim Generate a heatmap for pariwise similarity 5
heatmap2 6
helixturnhelix Report nucleic acid binding motifs 5
Hexamer frequency calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences 6
HHsearch detecting remote homologues of proteins 1
hicAdjustMatrix adjust the shape of a Hi-C matrix 6
hicAggregateContacts allow plotting of aggregated Hi-C contacts between regions specified in a file 10
hicAverageRegions sums Hi-C contacts around given reference points and computes their average. 6
hicBuildMatrix create a contact matrix 18
hicCompareMatrices normalize and compare two Hi-C contact matrices 11
hicCompartmentalization compute pairwise correlations between multiple Hi-C contact matrices 6
hicConvertFormat Convert between different file formats 7
hicCorrectMatrix run a Hi-C matrix correction algorithm 17
hicCorrelate compute pairwise correlations between multiple Hi-C contact matrices 15
hicDetectLoops searches for enriched regions 6
hicDifferentialTAD searches for differential TADs 2
hicFindRestSite identify restriction enzyme sites 7
hicFindTADs identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin 16
hicHyperoptDetectLoops optimizes parameters for hicDetectLoops 2
hicInfo get information about the content of a Hi-C matrix 6
hicMergeDomains Merges TAD domains 2
hicMergeLoops merge detected loops of different resolutions. 7
hicMergeMatrixBins merge adjacent bins from a Hi-C contact matrix to reduce its resolution 15
hicNormalize normalizes a matrix to norm range or smallest read count 7
hicPCA compute the principal components for A / B compartment analysis 12
hicPlotAverageRegions plot the average regions from hicAverageRegions 7
hicPlotDistVsCounts compute distance vs Hi-C counts plot per chromosome 15
hicPlotMatrix plot a Hi-C contact matrix heatmap 16
hicPlotSVL plots the relation of short vs long range contacts 6
hicPlotTADs plot Hi-C contact matrices heatmaps alongside other data tracks 9
hicPlotViewpoint plot interactions around a viewpoint 12
hicQuickQC get a first quality estimate of Hi-C data 7
hicSumMatrices combine Hi-C matrices of the same size 16
hicTransform transform a matrix to obs/exp, pearson and covariance matrices 12
Hicup Deduplicator removes duplicated di-tags (retaining one copy of each) from the data set. 4
Hicup Digester cuts throughout a selected genome at one or two specified restriction sites. 4
Hicup Filter classifies read pairs, identifying valid Hi-C di-tags 4
Hicup Mapper aligns paired reads independently to a reference genome and retains reads where both partners align. 4
Hicup Pipeline controls the other programs in the HiCUP pipeline. 4
Hicup Truncater terminates sequence reads at specified Hi-C ligation junctions. 4
hicValidateLocations validate detected loops with protein peaks. 6
Hierarchical clustering from MD RMSD matrix data 3
Hifiasm haplotype-resolved de novo assembler for PacBio Hifi reads 11
Hifiasm_meta for metagenome assembly using Hifi reads 2
hifive manipulate, analyze, and plot HiC and 5C chromatin interaction data 2
HighResPrecursorMassCorrector Corrects the precursor mass and charge determined by the instrument software. 5
HISAT2 A fast and sensitive alignment program 19
Histogram of a numeric column 4
Histogram equalization automatic histogram equalization 1
Histogram w ggplot2 7
HMDB MS search search by masses on HMDB online LCMS bank 6
HMM - determine essentiality of a genome 6
hmmalign align sequences to a profile HMM 7
hmmbuild Build a profile HMM from an input multiple alignment 8
hmmconvert convert profile file to a HMMER format 7
hmmemit sample sequence(s) from a profile HMM 7
hmmfetch retrieve profile HMM(s) from a file 7
hmmscan search sequence(s) against a profile database 8
hmmsearch search profile(s) against a sequence database 8
hmoment Hydrophobic moment calculation 5
Homology Classifier and Filter from a genetree using the ETE Toolkit 4
Homoscedasticity and normality Checks the homogeneity of the variance and the normality of the distribution 1
Homova Homogeneity of molecular variance 5
htseq-clip - A toolset for the analysis of eCLIP/iCLIP datasets 1
htseq-count - Count aligned reads in a BAM file that overlap features in a GFF file 9
Human Cell Atlas Matrix Downloader retrieves expression matrices and metadata from the Human Cell Atlas. 3
HUMAnN to profile presence/absence and abundance of microbial pathways and gene families Nucleic acid sequence analysis Phylogenetic analysis 2
HUMAnN2 to profile presence/absence and abundance of microbial pathways and gene families 5
HVIS visualization of genomic data with the Hilbert curve 2
Hydrogen Bond Analysis - analyze H-bonds between two segments 4
Hydrogen Bond Analysis using VMD between two segments of a trajectory 1
Hyperparameter Search performs hyperparameter optimization using various SearchCVs 11
HyPhy-aBSREL adaptive Branch Site Random Effects Likelihood 27
HyPhy-BGM - Detecting coevolving sites via Bayesian graphical models 26
HyPhy-BUSTED Branch-site Unrestricted Statistical Test for Episodic Diversification 26
HyPhy-CFEL Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches 6
HyPhy-Conv translate an in-frame codon alignment to proteins 5
HyPhy-FADE : FUBAR* Approach to Directional Evolution (*Fast Unconstrained Bayesian Approximation) 25
HyPhy-FEL Fixed Effects Likelihood 25
HyPhy-FUBAR Fast Unconstrained Bayesian AppRoximation 25
HyPhy-GARD Genetic Algorithm for Recombination Detection 26
HyPhy-MEME Mixed Effects Model of Evolution 25
HyPhy-PRIME Property Informed Models of Evolution 20
HyPhy-RELAX Detect relaxed selection in a codon-based phylogenetic framework 24
HyPhy-SLAC Single Likelihood Ancestor Counting 25
HyPhy-SM2019 Partition Tree using Modified Slatkin-Maddison Test 24
HyPhy-Summary generate summary report of HyPhy analyses 6
HyPo super fast and accurate polisher for long read genome assemblies 1
ID choice Choosing a particular column in your metadata to be considered as Identifiers 2
IDBA-HYBRID Iterative de Bruijn Graph Assembler for hybrid sequencing data 2
IDBA-TRAN Iterative de Bruijn Graph Assembler for transcriptome data 3
IDBA-UD Iterative de Bruijn Graph Assembler for data with highly uneven depth 3
IDConflictResolver Resolves ambiguous annotations of features with peptide identifications 5
idconvert Convert mass spectrometry identification files 4
IDDecoyProbability Estimates peptide probabilities using a decoy search strategy.WARNING: This util is deprecated. 3
Identification Parameters Sets the identification parameters to be used in SearchGUI and PeptideShaker apps 6
Identify optimal scoring subnetwork using Heinz 2
IdentifyPrimaryObjects identify biological objects of interest 2
IDExtractor Extracts 'n' peptides randomly or best 'n' from idXML files. 3
IDFileConverter Converts identification engine file formats. 6
IDFilter Filters results from protein or peptide identification engines based on different criteria. 6
IDMapper Assigns protein/peptide identifications to features or consensus features. 5
IDMassAccuracy Calculates a distribution of the mass error from given mass spectra and IDs. 5
IDMerger Merges several protein/peptide identification files into one file. 6
idpAssemble Merge IDPicker databases from single files into a merged database, and filters the result at PSM/spectrum/peptide/protein/gene levels. 4
idpEmbedder Embed human/mouse gene metadata into IDPicker files 4
IDPosteriorErrorProbability Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. 5
idpQonvert Prepare identification results for IDPicker 4
idpQuery Creates text reports from idpDB files. 5
IDR compare ranked list of identifications 2
IDR/OMERO Download - download images from any OMERO instance using image IDs 10
IDRipper Split protein/peptide identification file into several files according to annotated file origin. 4
IDRTCalibration Can be used to calibrate RTs of peptide hits linearly to standards. 4
IDScoreSwitcher Switches between different scores of peptide or protein hits in identification data 6
IDSplitter Splits protein/peptide identifications off of annotated data files 4
IdxStats reports stats of the BAM index file 8
IEDB MHC Binding prediction 3
iep Calculates the isoelectric point of a protein 5
Illuminapairedend - Assembling pair-end reads Construct consensus reads from Illumina pair-end reads 3
Image Converter 3
Image Info Show Image Info 2
Image Montage 3
Image Registration based on intensity information 3
ImageMath perform simple mathematical operations on images 2
Import Anndata and loom from different format 9
Inbreeding and kinship : Analyze the pedigree without genomic data 2
inchi-to-mol converter 2
InclusionExclusionListCreator Creates inclusion and/or exclusion lists. 2
Indicator Identify indicator "species" for nodes on a tree 5
Infer Experiment speculates how RNA-seq were configured 12
Infinium Human Methylation BeadChip Determines differentially methylated regions and positions from Infinium Methylation Assays 1
infoseq Displays some simple information about sequences 5
Initial processing using RaceID performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data 8
Inner Distance calculate the inner distance (or insert size) between two paired RNA reads 12
Insert indel qualities into a BAM file 4
Insertion Profile calculates the distribution of inserted nucleotides across reads 6
Insertion size metrics for PAIRED data 3
Inspect and manipulate with scanpy 7
Inspect AnnData object 10
Inspect Expression Set Object Inspect an ExpressionSet object by a variety of attributes 5
InspectAdapter Annotates MS/MS spectra using Inspect. 3
instaGRAAL Large genome reassembly based on Hi-C data 2
InStrain Compare Compares multiple inStrain profiles (popANI, coverage_overlap, etc.) Cross-assembly Genome comparison SNP detection 2
InStrain Profile Creates an inStrain profile (microdiversity analysis) from a mapping file Cross-assembly Genome comparison SNP detection 2
IntaRNA Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites. 4
Integron Finder is a program that detects integrons in DNA sequences Genome annotation Nucleic acid sequence feature detection Protein sequence feature detection Sequence motif recognition 2
Intensity Check Statistical measures, number of missing values and mean fold change 2
InternalCalibration Applies an internal mass recalibration. 5
InterProphet Combine Peptide Prophet results from multiple search engines 2
InterProScan functional annotation 9
Intersect multiple VCF datasets 2
Intersect the intervals of two datasets Filtering 6
Intersect intervals find overlapping intervals in various ways 22
IQ-TREE Phylogenomic / evolutionary tree construction from multiple sequences 7
Iris Refine insertion sequences 3
ISEScan Insertion Sequence Elements detection in prokaryotic genomes 1
IsobaricAnalyzer Calculates isobaric quantitative values for peptides 4
isochore Plots isochores in large DNA sequences 5
IsoformSwitchAnalyzeR statistical identification of isoform switching 1
Isoplot: Generate plots from isocor output 2
Iterative Mapping iteratively maps the raw reads of RNA structural data to the reference transcriptome 1
ITSx identifies ITS sequences and extracts the ITS region 1
ivar consensus Call consensus from aligned BAM file 9
ivar filtervariants Filter variants across replicates or multiple samples aligned using the same reference 7
ivar getmasked Detect primer mismatches and get primer indices for the amplicon to be masked 4
ivar removereads Remove reads from trimmed BAM file 11
ivar trim Trim reads in aligned BAM 13
ivar variants Call variants from aligned BAM file 9
IVR indicator 1
IWTomics Load Smooth and Plot 1
IWTomics Plot with Threshold on Test Scale 1
IWTomics Test and Plot 1
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 8
JAMM Calls peaks on NGS data 1
JasmineSV Merge structural variants across samples 2
JBrowse genome browser Map drawing Sequence visualisation 31
JBrowse - Data Directory to Standalone upgrades the bare data directory to a full JBrowse instance Conversion 30
Je-Clip clips Unique Molecular Identifiers (UMIs) from fastq files 2
Je-Demultiplex demultiplexes fastq files 2
Je-Demultiplex-Illu demultiplexes fastq files using Illumina Index file 2
Je-MarkDuplicates to filter BAM files for read duplicates taking UMIs into account 2
jellyfish 1
Join two files 12
Join HUMAnN2 generated tables 4
Join the intervals of two datasets side-by-side Aggregation 5
Join (merge) gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table Nucleic acid sequence analysis Phylogenetic analysis 2
Join +/- Ions Join positive and negative ionization-mode W4M datasets for the same samples 1
Join MAF blocks by Species 1
Join neighbors rapidly with RapidNJ 1
Join two Datasets side by side on a specified field 4
Join two files on column allowing a small difference 2
JQ process JSON 1
Junction Annotation compares detected splice junctions to reference gene model 12
Junction Saturation detects splice junctions from each subset and compares them to reference gene model 12
Kallisto pseudo - run pseudoalignment on RNA-Seq transcripts 6
Kallisto quant - quantify abundances of RNA-Seq transcripts 8
Karyotype Plotting tool for multiple series 1
Kc-Align 11
Kernel Canonical Correlation Analysis 2
Kernel Principal Component Analysis 2
khmer: Abundance Distribution Calculate abundance distribution of k-mers using pre-made k-mer countgraphs 4
khmer: Abundance Distribution (all-in-one) Calculate abundance distribution of k-mers 4
khmer: Count Median Count the median/avg k-mer abundance for each sequence 4
khmer: Extract partitions Separate sequences that are annotated with partitions into grouped files 4
khmer: Filter reads by minimal k-mer abundance 4
khmer: Filter reads below k-mer abundance of 50 4
khmer: Normalize By Median Filter reads using digital normalization via k-mer abundances Sequence file editing Sequence word comparison 5
khmer: Sequence partition all-in-one Load, partition, and annotate sequences 4
Kinfold Simulates the stochastic folding kinetics of RNA sequences into secondary structures. 1
KING Kinship-based INference for GWAS 2
Kinwalker cotranscriptional folding of RNAs 1
Kleborate screen genome assemblies of Klebsiella pneumoniae 1
KOBAS Annotate KEGG Orthology Based Annotation System 3
KOBAS Identify KEGG Orthology Based Annotation System 3
KofamScan gene function annotation based on KEGG orthology and HMM 2
Kraken assign taxonomic labels to sequencing reads 8
Kraken taxonomic report view report of classification for multiple samples 3
Kraken-biom Create BIOM-format tables from kraken output 2
Kraken-filter filter classification by confidence score 4
Kraken-mpa-report view report of classification for multiple samples 5
Kraken-report view sample report of a classification 5
Kraken-translate convert taxonomy IDs to names 4
Kraken2 assign taxonomic labels to sequencing reads 5
Krakentools: Calculates alpha diversity from the Bracken abundance estimation file 1
Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) from Kraken, Krona and Bracken files 1
Krakentools: Convert kraken report file to krona text file 1
Krona pie chart from taxonomic profile 10
Kronik processes Hardklor features to find peptides by chromatographic profiling 4
Label free protein summarisation and quantitation 1
Label to Points Converts label image to points 2
LabeledEval Evaluation tool for isotope-labeled quantitation experiments. 4
LAJ Pairwise Alignment Viewer 1
Landmark Registration Landmark Registration 5
LAST-split finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). 4
LAST-train finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. 5
LASTal finds local alignments between query sequences, and reference sequences. 6
LASTdb prepares sequences for subsequent comparison and alignment using lastal. 5
LASTZ : align long sequences 7
Lastz paired reads map short paired reads against reference sequence 2
LASTZ_D : estimate substitution scores matrix 5
LAV to BED Converts a LAV formatted file to BED format 1
LCMS matching Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. 3
LD linkage disequilibrium and tag SNPs 1
Lefse description 5
legsta Legionella pneumophila sequence based typing 2
Libshuff Cramer-von Mises tests communities for the same structure 5
lighter can correct the reads containing sequence errors 1
LightGBM - train and apply LightGBM models 3
limma Perform differential expression with limma-voom or limma-trend Differential gene expression profiling RNA-seq read count analysis 19
lindna Draws linear maps of DNA constructs 5
Line/Word/Character count of a dataset 1
Lineage Branch Analysis using StemID inspects branches of a lineage tree 6
Lineage computation using StemID generates lineage from prior clustering 6
Linear regression ajusted for autocorrelation in the residuals 1
LINKS - scaffold genome assemblies with long reads 1
Lipidmaps : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. 1
List Organisms in Apollo 8
List spaln parameter tables Given a query species, list the spaln settings tables that exist, from closest related species to most different 4
List.otulabels Lists otu labels from shared or relabund file 5
List.seqs Lists the names (accnos) of the sequences 5
Local Contributions to Beta Diversity (LCBD) Computes a measure of beta diversity, SCBD and representations 1
Local Threshold applies a local threshold algorithm to an image 2
LocARNA Multiple Alignment and Folding of RNAs 1
LocARNA Multiple Aligner Multiple Alignment and Folding of RNAs (mlocarna) 2
locarna_graphclust 3
Lofreq filter called variants posteriorly 4
Lordec is a set a programs for correcting sequencing errors in PacBio reads 5
lorikeet spoligotyping M. tuberculosis DNA fingerprinting 1
LotuS2 fast OTU processing pipeline 10
LowMemPeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra. 4
LowMemPeakPickerHiResRandomAccess Finds mass spectrometric peaks in profile mass spectra. 2
LowMemPeakPickerHiResRandomAccess Finds mass spectrometric peaks in profile mass spectra. 1
LPS LASSO-Patternsearch algorithm 1
LuciphorAdapter Modification site localisation using LuciPHOr2. 5
LUMPY is a probabilistic framework for structural variant discovery 2
LUMPY preprocessing extracts discordant read pairs and split-read alignments from a BAM dataset 2
MaAsLin 2 Microbiome Multivariable Association with Linear Models 1
Machine Learning Visualization Extension includes several types of plotting for machine learning 6
MACS Model-based Analysis of ChIP-Seq 4
MACS2 bdgbroadcall Call broad peaks from bedGraph output 9
MACS2 bdgcmp Deduct noise by comparing two signal tracks in bedGraph 9
MACS2 bdgdiff Differential peak detection based on paired four bedgraph files 10
MACS2 bdgpeakcall Call peaks from bedGraph output 9
MACS2 callpeak Call peaks from alignment results 12
MACS2 filterdup Remove duplicate reads at the same position 9
MACS2 predictd Predict 'd' or fragment size from alignment results 9
MACS2 randsample Randomly sample number or percentage of total reads 9
MACS2 refinepeak Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) 9
MAF Coverage Stats Alignment coverage information 3
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
MAF-convert read MAF-format alignments and write them in another format. 4
MAFFT Multiple alignment program for amino acid or nucleotide sequences 9
MAFFT add Align a sequence,alignment or fragments to an existing alignment. 6
MAGeCK count - collect sgRNA read counts from read mapping files 8
MAGeCK GSEA - a fast implementation of Gene Set Enrichment Analysis 4
MAGeCK mle - perform maximum-likelihood estimation of gene essentiality scores 5
MAGeCK pathway - given a ranked gene list, test whether one pathway is enriched 4
MAGeCKs test - given a table of read counts, perform the sgRNA and gene ranking 5
Magic-BLAST: map large RNA or DNA sequences against a whole genome or transcriptome 3
Mahotas-features Compute features using mahotas 1
Make Design Assign groups to Sets 5
Make File : Build a gd_snp or gd_genotype file 2
Make OTU table Make an OTU table from an OTU map and a taxonomy assignment file 1
Make phylogeny (make_phylogeny) 2
Make strain profiles Nucleic acid sequence analysis Phylogenetic analysis 2
Make strain profiles 3
Make taxonomy summary charts based on taxonomy assignment (plot_taxa_summary) 2
Make.biom Make biom files from a shared file 5
Make.contigs Aligns paired forward and reverse fastq files to contigs as fasta and quality 6
Make.fastq Convert fasta and quality to fastq 6
Make.group Make a group file 6
Make.lefse create a lefse formatted input file from mothur's output files 6
Make.lookup allows you to create custom lookup files for use with shhh.flows 5
Make.shared Make a shared file from a list and a group 5
Make.sra creates the necessary files for a NCBI submission 5
Maker genome annotation pipeline 10
MALDIquant peak detection Peak detection, binning and filtering for mass-spectrometry imaging data 7
MALDIquant preprocessing Preprocessing of mass-spectrometry imaging data 4
MALT analyzer 2
Manipulate AnnData object 10
Manipulate Expression Set Object Manipulate ExpressionSet objects by a variety of attributes 1
Manipulate FASTQ reads on various attributes Sequence conversion 4
Manipulate loom object Add layers, or row/column attributes to a loom file 7
Mantel Mantel correlation coefficient between two matrices. 5
Map annotation ids on a Maker annotation 5
Map diversity from remote sensing data 1
Map peptides to a bed file for viewing in a genome browser 3
map plot gridded (lat/lon) netCDF data 2
Map with BFAST 1
Map with Bowtie for Illumina 7
Map with Bowtie for SOLiD 1
Map with BWA - map short reads (< 100 bp) against reference genome 12
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 14
Map with KMA 2
Map with minimap2 A fast pairwise aligner for genomic and spliced nucleotide sequences Sequence alignment 18
Map with Mosaik 1
Map with PerM for SOLiD and Illumina 1
MapAlignerIdentification Corrects retention time distortions between maps based on common peptide identifications. 3
MapAlignerPoseClustering Corrects retention time distortions between maps using a pose clustering approach. 4
MapAlignerSpectrum Corrects retention time distortions between maps by spectrum alignment. 3
MapAlignerTreeGuided Tree guided correction of retention time distortions between maps. 2
MapBed apply a function to a column for each overlapping interval 21
MapNormalizer Normalizes peak intensities in an MS run. 4
Mapper for long, error-prone reads, like Nanopore ONT and PacBio 1
MapRTTransformer Applies retention time transformations to maps. 5
MapStatistics Extract extended statistics on the features of a map for quality control. 4
MaRaClusterAdapter Facilitate input to MaRaCluster and reintegrate. 2
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 17
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 16
marscan Finds MAR/SAR sites in nucleic sequences 5
MascotAdapter Annotates MS/MS spectra using Mascot. 4
MascotAdapterOnline Annotates MS/MS spectra using Mascot. 4
mash screen determines how well query sequences are contained within a pool of sequences 3
mash sketch Create a reduced representation of a sequence or set of sequences, based on min-hashes 1
maSigPro Significant Gene Expression Profile Differences in Time Course Gene Expression Data 5
maskfeat Mask off features of a sequence 5
MaskImage hide portions of an image based on previously identified objects 2
maskseq Mask off regions of a sequence 5
MassBank spectrum searches : Search by pseudo-spectra on a High Quality Mass Spectral Database. 1
MassCalculator Calculates masses and mass-to-charge ratios of peptide sequences 5
MassTraceExtractor Detects mass traces in centroided LC-MS data. 3
MasterVar to pgSnp Convert from MasterVar to pgSnp format 1
matcher Finds the best local alignments between two sequences 5
Matings : Assignment of optimal breeding pairs 2
Max SuCOS score - determine maximum SuCOS score of ligands against clustered fragment hits 7
MaxBin2 clusters metagenomic contigs into bins 4
MaxQuant Imputation Protein quantification Statistical calculation 17
MaxQuant (using mqpar.xml) Imputation Protein quantification Statistical calculation 9
MaxQuant Phosphopeptide ANOVA Runs ANOVA and KSEA for phosphopeptides. Dendrogram visualisation Enrichment analysis Heat map generation Protein interaction network analysis Standardisation and normalisation Statistical inference 2
MaxQuant Phosphopeptide Preprocessing Prep phosphoproteomic MaxQuant output for statistical anlaysis. Aggregation Conversion Sequence annotation Sequence database search 2
MCL The Markov Cluster Algorithm, a cluster algorithm for graphs Clustering 2
MCQUANT a module for single-cell data extraction 1
MDS Scatter Plot of molecule similarity 1
MDTraj file converter - interconvert between MD trajectory file formats. 5
MEA Predict MEA structures and compare structures of RNAs 1
MeanQualityByCycle chart distribution of base qualities 14
MeasureGranularity output spectra of size measurements of the textures 2
MeasureImageAreaOccupied measure the area in an image occupied by objects 2
MeasureImageIntensity measure several intensity features across an entire image 2
MeasureImageQuality measure features that indicate image quality 2
MeasureObjectIntensity measure several intensity features for identified objects 2
MeasureObjectSizeShape measure area and shape features of identified objects 2
MeasureTexture quantify the roughness and smoothness of the textures 2
medaka consensus pipeline Assembly polishing via neural networks 11
medaka consensus tool Assembly polishing via neural networks 10
medaka variant pipeline via neural networks 9
medaka variant tool decodes variant calls from medaka consensus output 14
Megablast compare short reads against htgs, nt, and wgs databases 2
MEGAHIT for metagenomics assembly 7
megahit contig2fastg for converting MEGAHIT's contigs (.fa) to assembly graphs (.fastg) 1
megamerger Merge two large overlapping nucleic acid sequences 5
MEGAN Blast2LCA: apply LCA alignment to produce a taxonomic classification 1
MEGAN: Extract reads by classification 1
MEGAN: Generate a MEGAN rma6 file from a DIAMOND or MALT sam file 2
MEGAN: Generate a MEGAN rma6 file from a DIAMOND daa file 2
MEGAN: Generate RMA files from BLAST output 2
MEGAN: Get information about a DIAMOND file 1
MEGAN: meganize a DIAMOND file for use with MEGAN 2
melt collapse combinations of variables:values to single lines 1
MEME - Multiple EM for Motif Elicitation 10
MEME psp-gen - perform discriminative motif discovery 6
MEME-ChIP - motif discovery, enrichment analysis and clustering on large nucleotide datasets 3
Merge multiple VCF datasets 2
Merge the overlapping intervals of a dataset Sequence merging 5
Merge MetaPhlAn abundance tables Nucleic acid sequence analysis Phylogenetic analysis 8
Merge BAM Files merges BAM files together 3
Merge BedGraph files 3
Merge Columns together 4
Merge GROMACS topologies and GRO files 7
Merge matching reads into clusters with TN-93 3
Merge Neighbours in Label Merge Neighbours in Label Image 2
Merge PCR duplicates according to UMIs 3
Merge peaklists produced by the tools 'Process scans (and SIM-Stitch)' or 'Replicate filter' 1
Merge.count Merge count tables 2
Merge.files Merge data 5
Merge.groups Merge groups in a shared file 5
Merge.sfffiles Merge SFF files 5
Merge.taxsummary Merge tax.summary files 6
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 14
merger Merge two overlapping nucleic acid sequences 5
MergeSamFiles merges multiple SAM/BAM datasets into one 14
Merging fragmented molecules 1
Merqury evaluate the assembly quality Genome assembly 4
Meryl a genomic k-mer counter and sequence utility Genome assembly 8
Mesmer Mesmer for whole-cell segmentation of multiplexed tissue imaging data 3
MetaBAT2 metagenome binning 3
MetaboliteAdductDecharger Decharges and merges different feature charge variants of the same metabolite. 3
MetaboliteSpectralMatcher Perform a spectral library search. 4
MetaEuk Easy Predict High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics 3
MetaGeneAnnotator gene-finding program for prokaryote and phage (used by sixgill) 1
Metagenome Contributions of OTUs to user-specified functions 2
metagenomeSeq Normalization Cumulative sum scaling 1
metaMS.runGC GC-MS data preprocessing using metaMS package 6
MetaNovo Produce targeted databases for mass spectrometry analysis. 2
MetaPhlAn to profile the composition of microbial communities Nucleic acid sequence analysis Phylogenetic analysis 7
MetaPhlAn2 to profile the composition of microbial communities 2
metaplasmidSPAdes extract and assembly plasmids from metagenomic data 6
MetaProSIP Performs proteinSIP on peptide features for elemental flux analysis. 6
MetaProteomeAnalyzer functional and taxonomic characterization of proteins 2
metaQuantome: create samples file by specifying the experiment's groups and associated column names 6
metaQuantome: database download the GO, EC, and NCBI databases 6
metaQuantome: expand a set of functional or taxonomy annotations 6
metaQuantome: filter for quality, redundancy, and sample coverage 6
metaQuantome: stat differential analysis of functional expression and taxonomic abundance 6
metaQuantome: visualize taxonomic analysis, functional analysis, and function-taxonomy analysis results 6
metaSPAdes metagenome assembler 12
Metastats generate principle components plot data 5
metaviralSPAdes extract and assembly viral genomes from metagenomic data 6
MetFrag in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra 3
MetFrag Vis Visualisation for MetFrag results 1
MethylDackel A tool for processing bisulfite sequencing alignments Gene methylation analysis 7
metilene calling differentially methylated regions from bisulfite sequencing data 5
MiGMAP mapper for full-length T- and B-cell repertoire sequencing 5
Mimarks.attributes Reads bioSample Attributes xml and generates source for get.mimarkspackage command 5
MiModD Convert converts sequence data into different formats 2
MiModD Coverage Statistics calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool 2
MiModD Deletion Calling (for PE data) predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes 2
MiModD Extract Variant Sites from a BCF file 2
MiModD File Information provides summary reports for supported sequence data formats. 3
MiModD NacreousMap maps phenotypically selected variants by multi-variant linkage analysis 3
MiModD Read Alignment maps sequence reads to a reference genome using SNAP 1
MiModD Rebase Sites from a VCF file 3
MiModD Reheader takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file 2
MiModD Report Variants in a human-friendly format that simplifies data exploration 3
MiModD Run Annotation writes run metadata in SAM format for attaching it to sequenced reads data 2
MiModD Sort takes a SAM/BAM dataset and generates a coordinate/name-sorted copy 2
MiModD Variant Calling generates a BCF file of position-specific variant likelihoods and coverage information based on a reference sequence and reads aligned against it 2
MiModD VCF Filter extracts lines from a vcf variant file based on field-specific filters 3
MINE - Maximal Information-based Nonparametric Exploration 2
Minfi DMP to find differentially methylated positions 1
Minfi DMR to find differentially methylated regions 1
Minfi Drop SNPs drop the probes that contain either a SNP at the CpG interrogation or at the single nucleotide extension 1
Minfi Get Beta obtain Beta value matrix 1
Minfi Get CN get the coordinating node associated with this D1Client object 1
Minfi Get M returns the Fisher information corresponding to a model and a design 1
Minfi Get SNPs retrieve the chromosome and the position of each SNP 1
Minfi Map to Genome mapping Ilumina methylation array data to the genome 1
Minfi Mset Create objects contains CpGs signals 1
Minfi Preprocess Funnorm implements the functional normalization algorithm 1
Minfi Preprocess Quantile implements stratified quantile normalization preprocessing 1
Minfi QC provides a simple quality control matrix and plot 1
Minfi Read 450k load .IDAT files 1
Minfi Rset store Beta values and/or M values 1
Minia Short-read assembler based on a de Bruijn graph 3
miniasm Ultrafast de novo assembly for long noisy reads 7
minipolish polishing miniasm assemblies 1
Miniprot align align a protein sequence against a genome with affine gap penalty, splicing and frameshift 2
Miniprot index build a genome index for miniprot 2
miRanda finds potential target sites for miRNAs in genomic sequences 3
MiRDeep2 identification of novel and known miRNAs 3
MiRDeep2 Mapper process and map reads to a reference genome 3
MiRDeep2 Quantifier fast quantitation of reads mapping to known miRBase precursors 2
miRNAture Computational detection of canonical microRNAs 1
Mismatch Profile calculates the distribution of mismatches across reads 6
Missing Values Sample Filter - Remove samples with a high percentage of missing values 2
MITObim mitochondrial baiting and iterative mapping 1
MitoHiFi assembly mitogenomes from Pacbio HiFi reads Genome assembly 1
MITOS de-novo annotation of metazoan mitochondrial genomes 2
MITOS2 de-novo annotation of metazoan mitochondrial genomes 3
mixmodel ANOVA for repeated measures statistics 1
MLST Scans genomes against PubMLST schemes 4
MLST List Lists available schemes for the MLST tool 4
MMPBSA/MMGBSA tool for estimating ligand binding affinities 7
MOABS MOdel based Analysis of Bisulfite Sequencing data 2
MOB-Recon Type contigs and extract plasmid sequences 2
MOB-Typer Get the plasmid type and mobility given its sequence 2
Model Prediction predicts on new data using a preffited model 7
Model temporal trend with a simple linear regression 1
Model Validation includes cross_validate, cross_val_predict, learning_curve, and more 11
Modify/convert GROMACS trajectories using trjconv and trjcat 8
moFF extracts MS1 intensities from spectrum files 5
mol2-to-mol converter 2
Molecule recognition in PDF documents (OSRA) 1
Molecule to fingerprint conversion to several different fingerprint formats 5
Monocle3 create a Monocle3 object from input data 4
Monocle3 diffExp of genes along a trajectory 4
Monocle3 learnGraph between cells in dimensionality reduced space 3
Monocle3 orderCells along trajectories 3
Monocle3 partition of cells into groups 3
Monocle3 plotCells in the reduced dimensionality space 5
Monocle3 preprocess a Monocle3 object to an initially dimensionally reduced space 3
Monocle3 reduceDim for downstream analysis 3
Monocle3 top markers for cell groups 1
Morpheus database search algorithm for high-resolution tandem mass spectra 2
mothur.ref.taxonomy-to-mothur.seq.taxonomy converter 2
Motif_Finder_Plot 2
mQC quality control of ribosome profiling mapping results 2
MRMMapper MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML) 4
MRMPairFinder Util which can be used to evaluate labeled pair ratios on MRM features. 5
MRMTransitionGroupPicker Picks peaks in SRM/MRM chromatograms. 5
MS-GF+ Identifies peptides in tandem mass spectra using the MS-GF+ search engine. 5
MSABOOT Output PHYLIP file with bootstrapped multiple sequence alignment data 3
msbar Mutate sequence beyond all recognition 5
msconvert Convert and/or filter mass spectrometry files 5
msconvert Subset Peak List against list of scan numbers or indices. 1
MSFraggerAdapter Peptide Identification with MSFragger.Important note:The Regents of the University of Michigan (“Michigan”) grants us permission to redistribute the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available for use on related service offerings supported by the University of Tubingen and the Center forIntegrative Bioinformatics. Per the license agreement the use of the pipeline and associated materials is for academic research, non-commercial or educational purposes. Any commercial use inquiries must be directed to the University of Michigan Technology Transfer Office at techtransfer@umich.edu. All right title and interest in MS Fragger shall remain with the University of Michigan.For details, please see the supplied license file or https://raw.githubusercontent.com/OpenMS/THIRDPARTY/master/All/MSFragger/License.txt 4
MSGFPlusAdapter MS/MS database search using MS-GF+. 6
MSI classification spatial classification of mass spectrometry imaging data 10
MSI colocalization mass spectrometry imaging colocalization 1
MSI combine combine several mass spectrometry imaging datasets into one 11
MSI data exporter exports imzML and Analyze7.5 to tabular files 7
MSI filtering tool for filtering mass spectrometry imaging data 8
MSI mz images mass spectrometry imaging m/z heatmaps 8
MSI plot spectra mass spectrometry imaging mass spectra plots 10
MSI preprocessing mass spectrometry imaging preprocessing 11
MSI Qualitycontrol mass spectrometry imaging QC 11
MSI segmentation mass spectrometry imaging spatial clustering 8
MSI single ion segmentation mass spectrometry imaging spatial DGMM 1
msms_extractor Extract MS/MS scans from the mzML file(s) based on PSM report 1
MSnbase readMSData Imports mass-spectrometry data files 3
msPurity.averageFragSpectra Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All) 6
msPurity.createDatabase Create and SQLite database of an LC-MS(/MS) experiment 6
msPurity.createMSP Create MSP files from msPurity processed data 6
msPurity.dimsPredictPuritySingle Calculate the anticipated precursor ion purity from a DIMS dataset. 6
msPurity.filterFragSpectra Filter fragmentations spectra associated with an XCMS feature 6
msPurity.flagRemove Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds (e.g. RSD of intensity and retention time). 6
msPurity.frag4feature Assign fragmentation spectra to XCMS features using msPurity 6
msPurity.purityA Assess acquired precursor ion purity of MS/MS spectra 6
msPurity.purityX Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset. 6
msPurity.spectralMatching Perform spectral matching to MS/MS spectral libraries 6
MSSimulator A highly configurable simulator for mass spectrometry experiments. 4
MSstats statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry 5
MSstatsConverter Converter to input for MSstats 2
MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling 4
MT2MQ Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome 3
Multi Compound Search an advanced molecular grep program using SMARTS 2
Multi Compound Search an advanced molecular grep program using SMARTS 1
Multi-Join (combine multiple files) 10
multiBamSummary calculates average read coverages for a list of two or more BAM/CRAM files 17
multiBigwigSummary calculates average scores for a list of two or more bigwig files 17
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
MultiplexResolver Completes peptide multiplets and resolves conflicts within them. 4
MultiQC aggregate results from bioinformatics analyses into a single report Statistical calculation Validation Visualisation 18
Multivariate PCA, PLS and OPLS 2
Mummer Align two or more sequences Read mapping Sequence alignment 5
MUMmer dotplot Combine mummer/nucmer/promer with mummerplot 4
Mummerplot Generate 2-D dotplot of aligned sequences Read mapping Sequence alignment 5
MUSCLE multiple aligner Multiple sequence alignment 2
MuSiC Compare estimate and compare cell type proportions in multiple sets of bulk RNA-seq data 2
MuSiC Deconvolution estimate cell type proportions in bulk RNA-seq data 4
MuSpinSim Configure define simulation parameters 2
MuSpinSim Plot plot values generated from MuSpinSim 2
MuSpinSim Simulate perform spin dynamics calculations for muon science experiments 2
Mutate Codons with SNPs 1
MyriMatch Identify peptides in tandem mass spectra. 4
MyriMatchAdapter Annotates MS/MS spectra using MyriMatch. 2
mz to sqlite Extract mzIdentML and associated proteomics datasets into a SQLite DB 5
MzMLSplitter Splits an mzML file into multiple parts 4
MzTabExporter Exports various XML formats to an mzTab file. 5
Naive Variant Caller (NVC) - tabulate variable sites from BAM datasets 5
NanoComporeDB Process SampComp results database 3
NanoPlot Plotting suite for Oxford Nanopore sequencing data and alignments 6
Nanopolish eventalign - Align nanopore events to reference k-mers 3
Nanopolish methylation - Classify nucleotides as methylated or not. 3
Nanopolish polyA - Estimate the length of the poly-A tail on direct RNA reads. 3
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 3
NanopolishComp: EventalignCollapse by kmers rather than by event 2
NanopolishComp: FreqMethCalculate calculates methylation frequency at genomic CpG sites 1
NASTIseq Identify cis-NATs using ssRNA-seq 1
Natural Product likeness calculator - calculates the similarity of the molecule to the structure space covered by known natural products 3
NCBI Accession Download Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 3
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 18
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 18
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 15
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 18
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 16
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 18
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 14
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 15
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 19
NCBI Datasets Gene download gene sequences and metadata 2
NCBI Datasets Genomes download genome sequence, annotation and metadata 12
NCBI ECitMatch search NCBI for citations in PubMed 5
NCBI EFetch fetch records from NCBI 5
NCBI EGQuery Provides the number of records retrieved in all Entrez databases by a single text query. 5
NCBI EInfo fetch NCBI database metadata 5
NCBI ELink link UIDs from one database to another 5
NCBI EPost post UIDs to NCBI History Server 5
NCBI ESearch search NCBI Databases by text query 5
NCBI ESummary fetch summary of history/ids 5
NCBI get species taxids 2
Nearest Neighbors Classification 2
Nearest Neighbors Classification 11
necat Error correction and de-novo assembly for ONT Nanopore reads 1
needle Needleman-Wunsch global alignment 5
neostore.zip-to-neostore converter 1
netboxr enables automated discovery of biological process modules by network analysis. 1
NetCDF timeseries Extractor Extract and plot time series 1
NetCDF xarray Coordinate Info Get values for each coordinate of a Netcdf file 4
NetCDF xarray map plotting Visualize netCDF variables on a geographical map 3
NetCDF xarray Metadata Info summarize content of a Netcdf file 5
NetCDF xarray operations manipulate xarray from netCDF and save back to netCDF 3
NetCDF xarray Selection extracts variable values with custom conditions on dimensions 5
newcpgreport Report CpG rich areas 5
newcpgseek Reports CpG rich region 5
Newick Display visualize a phylogenetic tree Phylogenetic tree visualisation 2
newseq Type in a short new sequence 5
NextAlign Viral genome sequence alignment 15
Nextclade Viral genome clade assignment, mutation calling, and sequence quality checks 18
NextDenovo string graph-based de novo assembler for long reads 1
NGSfilter Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers 3
nhmmer search a DNA model or alignment against a DNA database (BLASTN-like) 8
nhmmscan search DNA sequence(s) against a DNA profile database 8
Nmds generate non-metric multidimensional scaling data 6
NMR spectra alignment based on the Cluster-based Peak Alignment (CluPA) algorithm 2
NMR_Annotation Annotation of complex mixture NMR spectra and metabolite proportion estimation 1
NMR_Bucketing Bucketing and integration of NMR Bruker raw data 4
NMR_Normalization Normalization of NMR bucketed and integrated spectra 1
NMR_Preprocessing Preprocessing of 1D NMR spectra 4
NMR_Read Read Bruker NMR raw files 3
NoiseFilterGaussian Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data). 4
NoiseFilterSGolay Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. 5
Nonpareil to estimate average coverage and generate Nonpareil curves 2
noreturn Removes carriage return from ASCII files 5
Normalization Normalization of (preprocessed) spectra 4
Normalize combined meta'omic sequencing data Nucleic acid sequence analysis Phylogenetic analysis 2
Normalize combined meta'omic sequencing data 3
Normalize with scanpy 7
Normalize.shared Normalize the number of sequences per group to a specified level 5
NormalizeFasta normalize fasta datasets 14
notseq Exclude a set of sequences and write out the remaining ones 5
NOVOplasty de novo assembler for short circular genomes 3
NovorAdapter Template for Tool creation 3
NSPDK_candidateClusters 4
NSPDK_sparseVect 4
nthseq Writes one sequence from a multiple set of sequences 5
NucBed profile the nucleotide content of intervals in a FASTA file 21
NucleicAcidSearchEngine Annotate nucleic acid identifications to MS/MS spectra. 2
Nucleosome Predictions 1
Nucleotide Diversity : &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
Ocean biodiversity indicators from OBIS 2
ococo consensus caller on SAM/BAM 1
octanol Displays protein hydropathy 5
oddcomp Find protein sequence regions with a biased composition 5
odgi build construct a dynamic succinct variation graph 2
odgi viz variation graph visualizations 2
OGR Informations lists information about an OGR supported data source 2
OGR2ogr converts simple features data between file formats 2
OMSSAAdapter Annotates MS/MS spectra using OMSSA. 2
Online data fetching ... 2
ont_fast5_api: Compress multi read file(s) 2
ont_fast5_api: Multi to single read file(s) 2
ont_fast5_api: Single to multi read file(s) 2
ont_fast5_api: Subset of multi read file(s) 3
Open 3D Align with RDKit 2
Open Molecule Generator - exhaustive generation of chemical structures 3
OpenDUck chunk for dynamic undocking 1
OpenPepXL Tool for protein-protein cross-linking identification using labeled linkers. 4
OpenPepXLLF Tool for protein-protein cross linking with label-free linkers. 3
OpenSwathAnalyzer Picks peaks and finds features in an SWATH-MS or SRM experiment. 4
OpenSwathAssayGenerator Generates assays according to different models for a specific TraML 4
OpenSwathChromatogramExtractor Extract chromatograms (XIC) from a MS2 map file. 3
OpenSwathConfidenceScoring Compute confidence scores for OpenSwath results 5
OpenSwathDecoyGenerator Generates decoys according to different models for a specific TraML 5
OpenSwathDIAPreScoring Scoring spectra using the DIA scores. 4
OpenSwathFeatureXMLToTSV Converts a featureXML to a mProphet tsv. 4
OpenSwathFileSplitter Splits SWATH files into n files, each containing one window. 5
OpenSwathMzMLFileCacher This tool caches the spectra and chromatogram data of an mzML to disk. 4
OpenSwathRewriteToFeatureXML Combines featureXML and mProphet tsv to FDR filtered featureXML. 5
OpenSwathRTNormalizer This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. 5
OpenSwathWorkflow Complete workflow to run OpenSWATH 4
Operate on pixels with a mathematical expression 2
OPLS-DA_Contrasts OPLS-DA Contrasts of Univariate Results 5
OptiType HLA genotyping predictions from NGS data 1
ORFipy a versatile ORF finder 2
OrthoFinder finds orthogroups in a set of proteomes 7
Otu.association Calculate the correlation coefficient for the otus 5
Otu.hierarchy Relate OTUs at different distances 5
Overall FST : Estimate the relative fixation index between two populations 4
Overlay Images for visualization 2
OverlayOutlines places outlines of objects over a desired image. 2
Owler fast, trimmed overlap pipeline without aligning 1
PACKMOL - initial configurations for molecular dynamics simulations by packing optimization 2
PaDEL descriptor calculator 1
Paired Read Mate Fixer for paired data 3
Paired-end histogram of insert size frequency 1
Pairs sequenced : Offspring estimated heterozygosity of sequenced pairs 2
Pairwise intersection and heatmap for genomic intervals 4
Pairwise.seqs calculate uncorrected pairwise distances between sequences 5
palindrome Looks for inverted repeats in a nucleotide sequence 5
Pangolin Phylogenetic Assignment of Outbreak Lineages 22
Parallel Coordinates Plot of tabular data 3
PARalyzer A method to map interaction sites between RNA-binding proteins and their targets 1
ParmChk2 - Amber's parameter checker 8
parquet-to-csv converter 1
Parse blast XML output 2
Parse mitochondrial blast overlap-conscious coverage calculation between scaffold-accession number pairs from blast output 2
parse mykrobe predict for Shigella sonnei and tabulate results into a single tab-delimited file 1
Parse.list Generate a List file for each group 5
Parsimony Describes whether two or more communities have the same structure 5
Partition genes into expression clusters after differential expression analysis using a Trinity assembly 12
PASS significant transcription factor binding sites from ChIP data 1
Paste two files side by side 1
pasteseq Insert one sequence into another 5
Pathifier : Quantify deregulation of pathways in cancer 1
Pathview for pathway based data integration and visualization 3
Pathway Image : Draw a KEGG pathway, highlighting specified gene modules 3
Pathway Matcher PathwayMatcher is a software tool to search for pathways related to a list of proteins in Reactome. 3
patmatdb Search a protein sequence with a motif 5
PCA : Principal Component Analysis of genotype data 3
Pca Principal Coordinate Analysis for a shared file 6
PCA - principal component analysis using Bio3D 2
PCA plot w ggplot2 7
PCA visualization - generate trajectories of principal components of atomic motion 2
Pcoa Principal Coordinate Analysis for a distance matrix 5
Pcr.seqs Trim sequences 6
pdb-to-gro converter 1
PDBFixer to automatically fix a PDB file before performing molecular dynamics simulation 1
PEAKachu Calls Peaks in CLIP data 3
PeakPickerHiRes Finds mass spectrometric peaks in profile mass spectra. 4
PeakPickerIterative Finds mass spectrometric peaks in profile mass spectra. 4
PeakPickerWavelet Finds mass spectrometric peaks in profile mass spectra. 5
Pear Paired-End read merger 5
pepcoil Predicts coiled coil regions 5
pepinfo Plots simple amino acid properties in parallel 5
pepnet Displays proteins as a helical net 5
PepNovoAdapter Adapter to PepNovo supporting all PepNovo command line parameters. The results are converted from the PepNovo text outfile format into the idXML format. 2
PepPointer classify genomic location of peptides 2
PepQuery Peptide-centric search engine for novel peptide identification and validation. 4
pepstats Protein statistics 5
Peptide Genomic Coordinate Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB 2
Peptide Prophet Calculate Peptide Prophet statistics on search results 2
Peptide Shaker Perform protein identification using various search engines based on results from SearchGUI 19
PeptideIndexer Refreshes the protein references for all peptide hits. 6
pepwheel Shows protein sequences as helices 5
pepwindow Displays protein hydropathy 5
pepwindowall Displays protein hydropathy of a set of sequences 5
Per-SNP FSTs : Compute a fixation index score for each SNP 3
Percolator accurate peptide identification 2
PercolatorAdapter Facilitate input to Percolator and reintegrate. 2
Perform alpha rarefaction (alpha_rarefaction) 2
Perform Best-subsets Regression 2
Perform closed-reference OTU picking 1
Perform jackknifed UPGMA clustering and building jackknifed PCoA plots (jackknifed_beta_diversity) 2
Perform LDA Linear Discriminant Analysis 2
Perform metadata association on HUMAnN generated table Nucleic acid sequence analysis Phylogenetic analysis 2
Perform open-reference OTU picking 1
Perform open-reference OTU picking (pick_open_reference_otus) 2
Perform OTU picking (pick_otus) 2
Perform taxonomy summaries and plots (summarize_taxa_through_plots) 2
Permutate image along an axis 2
Personal Cancer Genome Reporter 1
PfamScan search a FASTA sequence against a library of Pfam HMM 1
pgma_graphclust 3
Pharmacophore generation (Align-it) 3
Pharmacophore alignment and optimization (Align-it) 3
pharmCAT Pharmacogenomics Clinical Annotation Tool 2
phmmer search a protein sequence against a protein database (BLASTP-like) 8
PhosphoScoring Scores potential phosphorylation sites in order to localize the most probable sites. 4
Phylip : prepare data for phylogenetic analysis 2
Phylo.diversity Alpha Diversity calculates unique branch length 5
Phylogenetic Tree : Show genetic relationships among individuals 3
phyloP interspecies conservation scores 1
Phyloseq: plot alpha diverstiy measure 1
Phyloseq: plot ordination 1
Phylotype Assign sequences to OTUs based on taxonomy 5
PhyML Phylogeny software based on the maximum-likelihood method. Phylogenetic analysis Phylogenetic inference (from molecular sequences) 4
Phyogenetic reconstruction with RAxML - Maximum Likelihood based inference of large phylogenetic trees 6
Picard Collect Sequencing Artifact Metrics Collect metrics to quantify single-base sequencing artifacts 6
Pick diverse compounds from a library with Butina clustering 2
Pick Primers : Find suitable PCR primers for SNPs 2
Pick representative set of sequences (pick_rep_set) 2
Pileup-to-Interval condenses pileup format into ranges of bases 4
pilon An automated genome assembly improvement and variant detection tool 2
Pipeline Builder an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers 11
PIPmiR PIPELINE a method to identify novel plant miRNA 1
Piranha peak-caller for CLIP- and RIP-Seq data 1
pizzly - fast fusion detection using kallisto 2
PlasFlow Prediction of plasmid sequences in metagenomic contigs 1
PlasmidFinder Plasmid identification in bacteria. 1
plasmidSPAdes extract and assembly plasmids from WGS data 6
plink 6
Plot with scanpy 8
Plot abundance with trend line 1
Plot actual vs predicted curves and residual plots of tabular data 1
Plot confusion matrix, precision, recall and ROC and AUC curves of tabular data 2
Plot heatmap of OTU table (make_otu_heatmap) 2
Plot performance per cell in nanopore reads 2
Plot signals for nanopore reads 2
plotcon Plot quality of conservation of a sequence alignment 5
plotCorrelation Create a heatmap or scatterplot of correlation scores between different samples 16
plotCoverage assesses the sequencing depth of BAM/CRAM files 16
plotDEXSeq Visualization of the per gene DEXSeq results 5
plotEnrichment plots read/fragment coverage over sets of regions 12
plotFingerprint plots profiles of BAM files; useful for assesing ChIP signal strength 17
plotHeatmap creates a heatmap for score distributions across genomic regions 17
plotorf Plot potential open reading frames 5
plotPCA Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output 16
plotProfile creates a profile plot for score distributions across genomic regions 16
Plotting tool for multiple series and graph types 5
PMIDs to PubTator binary matrix 1
Points to Binary Image Converts points to a binary image 1
Points to Label Points to Label Image 1
Points to Label Points to Label Image 1
Poisson two-sample test 1
polydot Displays all-against-all dotplots of a set of sequences 5
Polypolish Short-read polishing of long-read bacterial genome assemblies 1
Population Complexity : Evaluate possible numbers of ancestral populations 2
Porechop adapter trimmer for Oxford Nanopore reads 3
Pout2mzid add Percolator scoring to mzIdentML 2
Pre.cluster Remove sequences due to pyrosequencing errors 5
PrecursorIonSelector PrecursorIonSelector 4
PrecursorMassCorrector Corrects the precursor entries of MS/MS spectra, by using MS1 information. 5
Predict Metagenome based on the abundance of OTUs and a functional database 2
Predict variant effects with VEP 3
preg Regular expression search of a protein sequence 6
Prepare Input : Filter and convert to the format needed for these tools 4
Prepare ligand for docking with Autodock Vina 1
Prepare ligands for docking Tool to prepare ligands for docking with tools like Autodock Vina 4
Prepare receptor Tool to prepare receptor for docking with Autodock Vina 2
Preprocess raw feature vectors into standardized datasets 12
Preprocess population data for evolution trend analyzes 2
Preprocess sentinel 2 data read, crop, resample and write it as a raster stack 1
Preprocessing 4
Presence-absence and abundance Community abundance map, presence barplot and rarefaction curves 1
Pretext Snapshot 2
PretextMap converts SAM or BAM files into genome contact maps 7
prettyplot Displays aligned sequences, with colouring and boxing 5
prettyseq Output sequence with translated ranges 5
Primer.design identify sequence fragments that are specific to particular OTUs 5
primersearch Searches DNA sequences for matches with primer pairs 5
Principal component analysis with scikit-learn 3
Principal Component Analysis 1
PRINSEQ to process quality of sequences 5
ProbMetab Tool Wrapper function for ProbMetab R package. 2
Process Scans (and SIM-Stitch) - Read, filter and average MS scans 2
Process single-cell intensities Options to correct for exposure time, autofluorescence subtraction, or compute signal-to-background ratio. 1
proFIA Preprocessing of FIA-HRMS data 2
Profile Annotations for a set of genomic intervals 1
progressiveMauve constructs multiple genome alignments 3
Projective Transformation Projective Transformation 4
Projective Transformation of input points 5
Prokka Prokaryotic genome annotation Coding region prediction Gene prediction Genome annotation 11
Promoter 2.0 Find eukaryotic PolII promoters in DNA sequences 5
prot-scriber Protein annotation of short human readable descriptions 3
Protease prediction based on cleavage sites 3
Protein Database Downloader 6
Protein Prophet Calculate Protein Prophet statistics on search results 2
ProteinInference Protein inference based on the number of identified peptides. 4
Proteinortho detects orthologous proteins/genes within different species 5
Proteinortho grab proteins finds genes/proteins in a given fasta file 5
Proteinortho summary summaries the orthology-pairs/RBH files 5
ProteinQuantifier Compute peptide and protein abundances 4
ProteinResolver protein inference 4
Proteomiqon JoinQuantPepIonsWithProteins combines the results from ProteinInference and PSMBasedQuantification. 1
Proteomiqon LabeledProteinQuantification estimates protein abundances using quantified peptide ions. 1
Proteomiqon LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions. 1
ProteomIQon MzMLToMzLite converts mzML files to mzLite files. 2
ProteomIQon PeptideDB creates a peptide database in the SQLite format. 1
ProteomIQon PeptideSpectrumMatching iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches. 1
ProteomIQon ProteinInference uses identified peptides to infere proteins explaining their presence in the sample. 1
Proteomiqon PSMBasedQuantification allows label-free quantification as well as quantification of full metabolic labeled samples. 2
ProteomIQon PSMStatistics utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score. 3
PSM-Fragment Validator Validate PSMs against Ion Fragmentation 2
PSMFeatureExtractor Computes extra features for each input PSM. 5
psortb Determines sub-cellular localisation of bacterial/archaeal protein sequences 5
PTModel Trains a model for the prediction of proteotypic peptides from a training set. 4
PTPredict predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel 2
PubChem Assay Downloader as canonical SMILES 3
PubChem Download as canonical SMILES 3
PubMed query download a defined number of abstracts or PMIDs from PubMed 1
PureCLIP - HMM based peak caller designed for eCLIP/iCLIP data 2
Purge overlaps and haplotigs in an assembly based on read depth (purge_dups) 6
Pycoqc 1
pyGenomeTracks plot genomic data tracks 12
PyIron meta tools 1
PyMuonSuite AIRSS Cluster run clustering for optimised structures 2
PyMuonSuite AIRSS Configure define AIRSS parameters 2
PyMuonSuite AIRSS DFTB+ Optimise run DFTB+ optimisation 2
PyMuonSuite AIRSS Generate generate muonated structures 2
PyMuonSuite AIRSS UEP Optimise run UEP optimisation 2
PyMuonSuite Phonons calculate phonons using ASE and DFTB+ 2
PyMuonSuite Symmetry generate Wyckoff points symmetry report 2
PyProphet export Export tabular files, optional swath2stats export 2
PyProphet merge Merge multiple osw files 1
PyProphet peptide Peptide error-rate estimation 1
PyProphet protein Protein error-rate estimation 1
PyProphet score Error-rate estimation for MS1, MS2 and transition-level data 3
PyProphet subsample Subsample OpenSWATH file 1
pysradb search sequence metadata from SRA/ENA 2
pyteomics convert mztab to tabular Conversion 1
QCCalculator Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection. 5
QCEmbedder Attaches a table or an image to a given qc parameter. 4
QCExporter Will extract several qp from several run/sets in a tabular format. 4
QCExtractor Extracts a table attachment to a given qc parameter. 4
QCImporter Imports tables with quality control parameters into qcml files. 4
QCMerger Merges two qcml files together. 5
QCShrinker This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report. 4
QECB-Dissimilarity indicator 1
qiime2 alignment mafft De novo multiple sequence alignment with MAFFT 2
qiime2 alignment mafft-add Add sequences to multiple sequence alignment with MAFFT. 2
qiime2 alignment mask Positional conservation and gap filtering. 2
qiime2 composition add-pseudocount Add pseudocount to table 2
qiime2 composition ancom Apply ANCOM to identify features that differ in abundance. 2
qiime2 composition ancombc Analysis of Composition of Microbiomes with Bias Correction 1
qiime2 composition tabulate View tabular output from ANCOM-BC. 1
qiime2 cutadapt demux-paired Demultiplex paired-end sequence data with barcodes in-sequence. 2
qiime2 cutadapt demux-single Demultiplex single-end sequence data with barcodes in-sequence. 2
qiime2 cutadapt trim-paired Find and remove adapters in demultiplexed paired-end sequences. 2
qiime2 cutadapt trim-single Find and remove adapters in demultiplexed single-end sequences. 2
qiime2 dada2 denoise-ccs Denoise and dereplicate single-end Pacbio CCS 2
qiime2 dada2 denoise-paired Denoise and dereplicate paired-end sequences 2
qiime2 dada2 denoise-pyro Denoise and dereplicate single-end pyrosequences 2
qiime2 dada2 denoise-single Denoise and dereplicate single-end sequences 2
qiime2 deblur denoise-16S Deblur sequences using a 16S positive filter. 1
qiime2 deblur denoise-other Deblur sequences using a user-specified positive filter. 2
qiime2 deblur visualize-stats Visualize Deblur stats per sample. 2
qiime2 demux emp-paired Demultiplex paired-end sequence data generated with the EMP protocol. 2
qiime2 demux emp-single Demultiplex sequence data generated with the EMP protocol. 2
qiime2 demux filter-samples Filter samples out of demultiplexed data. 2
qiime2 demux subsample-paired Subsample paired-end sequences without replacement. 2
qiime2 demux subsample-single Subsample single-end sequences without replacement. 2
qiime2 demux summarize Summarize counts per sample. 2
qiime2 diversity adonis adonis PERMANOVA test for beta group significance 2
qiime2 diversity alpha Alpha diversity 2
qiime2 diversity alpha-correlation Alpha diversity correlation 2
qiime2 diversity alpha-group-significance Alpha diversity comparisons 2
qiime2 diversity alpha-phylogenetic Alpha diversity (phylogenetic) 2
qiime2 diversity alpha-rarefaction Alpha rarefaction curves 2
qiime2 diversity beta Beta diversity 2
qiime2 diversity beta-correlation Beta diversity correlation 2
qiime2 diversity beta-group-significance Beta diversity group significance 2
qiime2 diversity beta-phylogenetic Beta diversity (phylogenetic) 2
qiime2 diversity beta-rarefaction Beta diversity rarefaction 2
qiime2 diversity bioenv bioenv 2
qiime2 diversity core-metrics Core diversity metrics (non-phylogenetic) 2
qiime2 diversity core-metrics-phylogenetic Core diversity metrics (phylogenetic and non-phylogenetic) 2
qiime2 diversity filter-distance-matrix Filter samples from a distance matrix. 2
qiime2 diversity mantel Apply the Mantel test to two distance matrices 2
qiime2 diversity pcoa Principal Coordinate Analysis 2
qiime2 diversity pcoa-biplot Principal Coordinate Analysis Biplot 2
qiime2 diversity procrustes-analysis Procrustes Analysis 2
qiime2 diversity tsne t-distributed stochastic neighbor embedding 2
qiime2 diversity umap Uniform Manifold Approximation and Projection 2
qiime2 diversity-lib alpha-passthrough Alpha Passthrough (non-phylogenetic) 2
qiime2 diversity-lib beta-passthrough Beta Passthrough (non-phylogenetic) 2
qiime2 diversity-lib beta-phylogenetic-meta-passthrough Beta Phylogenetic Meta Passthrough 2
qiime2 diversity-lib beta-phylogenetic-passthrough Beta Phylogenetic Passthrough 2
qiime2 diversity-lib bray-curtis Bray-Curtis Dissimilarity 2
qiime2 diversity-lib faith-pd Faith's Phylogenetic Diversity 2
qiime2 diversity-lib jaccard Jaccard Distance 2
qiime2 diversity-lib observed-features Observed Features 2
qiime2 diversity-lib pielou-evenness Pielou's Evenness 2
qiime2 diversity-lib shannon-entropy Shannon's Entropy 2
qiime2 diversity-lib unweighted-unifrac Unweighted Unifrac 2
qiime2 diversity-lib weighted-unifrac Weighted Unifrac 2
qiime2 emperor biplot Visualize and Interact with Principal Coordinates Analysis Biplot 2
qiime2 emperor plot Visualize and Interact with Principal Coordinates Analysis Plots 2
qiime2 emperor procrustes-plot Visualize and Interact with a procrustes plot 2
qiime2 feature-classifier blast BLAST+ local alignment search. 2
qiime2 feature-classifier classify-consensus-blast BLAST+ consensus taxonomy classifier 2
qiime2 feature-classifier classify-consensus-vsearch VSEARCH-based consensus taxonomy classifier 2
qiime2 feature-classifier classify-hybrid-vsearch-sklearn ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier 2
qiime2 feature-classifier classify-sklearn Pre-fitted sklearn-based taxonomy classifier 2
qiime2 feature-classifier extract-reads Extract reads from reference sequences. 2
qiime2 feature-classifier find-consensus-annotation Find consensus among multiple annotations. 2
qiime2 feature-classifier fit-classifier-naive-bayes Train the naive_bayes classifier 2
qiime2 feature-classifier fit-classifier-sklearn Train an almost arbitrary scikit-learn classifier 2
qiime2 feature-classifier vsearch-global VSEARCH global alignment search 2
qiime2 feature-table core-features Identify core features in table 2
qiime2 feature-table filter-features Filter features from table 2
qiime2 feature-table filter-features-conditionally Filter features from a table based on abundance and prevalence 2
qiime2 feature-table filter-samples Filter samples from table 2
qiime2 feature-table filter-seqs Filter features from sequences 2
qiime2 feature-table group Group samples or features by a metadata column 2
qiime2 feature-table heatmap Generate a heatmap representation of a feature table 2
qiime2 feature-table merge Combine multiple tables 2
qiime2 feature-table merge-seqs Combine collections of feature sequences 2
qiime2 feature-table merge-taxa Combine collections of feature taxonomies 2
qiime2 feature-table presence-absence Convert to presence/absence 2
qiime2 feature-table rarefy Rarefy table 2
qiime2 feature-table relative-frequency Convert to relative frequencies 2
qiime2 feature-table rename-ids Renames sample or feature ids in a table 2
qiime2 feature-table subsample Subsample table 2
qiime2 feature-table summarize Summarize table 2
qiime2 feature-table tabulate-seqs View sequence associated with each feature 2
qiime2 feature-table transpose Transpose a feature table. 2
qiime2 fragment-insertion classify-otus-experimental Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. 2
qiime2 fragment-insertion filter-features Filter fragments in tree from table. 2
qiime2 fragment-insertion sepp Insert fragment sequences using SEPP into reference phylogenies. 2
qiime2 gneiss assign-ids Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. 2
qiime2 gneiss correlation-clustering Hierarchical clustering using feature correlation. 2
qiime2 gneiss dendrogram-heatmap Dendrogram heatmap. 2
qiime2 gneiss gradient-clustering Hierarchical clustering using gradient information. 2
qiime2 gneiss ilr-hierarchical Isometric Log-ratio Transform applied to a hierarchical clustering 2
qiime2 gneiss ilr-phylogenetic Isometric Log-ratio Transform applied to a phylogenetic tree 2
qiime2 gneiss ilr-phylogenetic-differential Differentially abundant Phylogenetic Log Ratios. 2
qiime2 gneiss ilr-phylogenetic-ordination Ordination through a phylogenetic Isometric Log Ratio transform. 2
qiime2 longitudinal anova ANOVA test 2
qiime2 longitudinal feature-volatility Feature volatility analysis 2
qiime2 longitudinal first-differences Compute first differences or difference from baseline between sequential states 2
qiime2 longitudinal first-distances Compute first distances or distance from baseline between sequential states 2
qiime2 longitudinal linear-mixed-effects Linear mixed effects modeling 2
qiime2 longitudinal maturity-index Microbial maturity index prediction. 2
qiime2 longitudinal nmit Nonparametric microbial interdependence test 2
qiime2 longitudinal pairwise-differences Paired difference testing and boxplots 2
qiime2 longitudinal pairwise-distances Paired pairwise distance testing and boxplots 2
qiime2 longitudinal plot-feature-volatility Plot longitudinal feature volatility and importances 2
qiime2 longitudinal volatility Generate interactive volatility plot 2
qiime2 metadata distance-matrix Create a distance matrix from a numeric Metadata column 2
qiime2 metadata shuffle-groups Shuffle values in a categorical sample metadata column. 2
qiime2 metadata tabulate Interactively explore Metadata in an HTML table 2
qiime2 phylogeny align-to-tree-mafft-fasttree Build a phylogenetic tree using fasttree and mafft alignment 2
qiime2 phylogeny align-to-tree-mafft-iqtree Build a phylogenetic tree using iqtree and mafft alignment. 2
qiime2 phylogeny align-to-tree-mafft-raxml Build a phylogenetic tree using raxml and mafft alignment. 2
qiime2 phylogeny fasttree Construct a phylogenetic tree with FastTree. 2
qiime2 phylogeny filter-table Remove features from table if they're not present in tree. 2
qiime2 phylogeny filter-tree Remove features from tree based on metadata 2
qiime2 phylogeny iqtree Construct a phylogenetic tree with IQ-TREE. 2
qiime2 phylogeny iqtree-ultrafast-bootstrap Construct a phylogenetic tree with IQ-TREE with bootstrap supports. 2
qiime2 phylogeny midpoint-root Midpoint root an unrooted phylogenetic tree. 2
qiime2 phylogeny raxml Construct a phylogenetic tree with RAxML. 2
qiime2 phylogeny raxml-rapid-bootstrap Construct a phylogenetic tree with bootstrap supports using RAxML. 2
qiime2 phylogeny robinson-foulds Calculate Robinson-Foulds distance between phylogenetic trees. 2
qiime2 quality-control bowtie2-build Build bowtie2 index from reference sequences. 2
qiime2 quality-control evaluate-composition Evaluate expected vs. observed taxonomic composition of samples 2
qiime2 quality-control evaluate-seqs Compare query (observed) vs. reference (expected) sequences. 2
qiime2 quality-control evaluate-taxonomy Evaluate expected vs. observed taxonomic assignments 2
qiime2 quality-control exclude-seqs Exclude sequences by alignment 2
qiime2 quality-control filter-reads Filter demultiplexed sequences by alignment to reference database. 2
qiime2 quality-filter q-score Quality filter based on sequence quality scores. 2
qiime2 sample-classifier classify-samples Train and test a cross-validated supervised learning classifier. 2
qiime2 sample-classifier classify-samples-from-dist Run k-nearest-neighbors on a labeled distance matrix. 2
qiime2 sample-classifier classify-samples-ncv Nested cross-validated supervised learning classifier. 2
qiime2 sample-classifier confusion-matrix Make a confusion matrix from sample classifier predictions. 2
qiime2 sample-classifier fit-classifier Fit a supervised learning classifier. 2
qiime2 sample-classifier fit-regressor Fit a supervised learning regressor. 2
qiime2 sample-classifier heatmap Generate heatmap of important features. 2
qiime2 sample-classifier metatable Convert (and merge) positive numeric metadata (in)to feature table. 2
qiime2 sample-classifier predict-classification Use trained classifier to predict target values for new samples. 2
qiime2 sample-classifier predict-regression Use trained regressor to predict target values for new samples. 2
qiime2 sample-classifier regress-samples Train and test a cross-validated supervised learning regressor. 2
qiime2 sample-classifier regress-samples-ncv Nested cross-validated supervised learning regressor. 2
qiime2 sample-classifier scatterplot Make 2D scatterplot and linear regression of regressor predictions. 2
qiime2 sample-classifier split-table Split a feature table into training and testing sets. 2
qiime2 sample-classifier summarize Summarize parameter and feature extraction information for a trained estimator. 2
qiime2 taxa barplot Visualize taxonomy with an interactive bar plot 2
qiime2 taxa collapse Collapse features by their taxonomy at the specified level 2
qiime2 taxa filter-seqs Taxonomy-based feature sequence filter. 2
qiime2 taxa filter-table Taxonomy-based feature table filter. 2
qiime2 tools export Export data from a QIIME 2 artifact 2
qiime2 tools import Import data into a QIIME 2 artifact 2
qiime2 vsearch cluster-features-closed-reference Closed-reference clustering of features. 2
qiime2 vsearch cluster-features-de-novo De novo clustering of features. 2
qiime2 vsearch cluster-features-open-reference Open-reference clustering of features. 2
qiime2 vsearch dereplicate-sequences Dereplicate sequences. 2
qiime2 vsearch fastq-stats Fastq stats with vsearch. 2
qiime2 vsearch merge-pairs Merge paired-end reads. 1
qiime2 vsearch uchime-denovo De novo chimera filtering with vsearch. 2
qiime2 vsearch uchime-ref Reference-based chimera filtering with vsearch. 2
QualiMap BamQC 5
QualiMap Counts QC 2
QualiMap Multi-Sample BamQC 2
QualiMap RNA-Seq QC 3
Quality format converter (ASCII-Numeric) 3
Quality Metrics Metrics and graphics to check the quality of the data 2
QualityControl Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get. 2
QualityScoreDistribution chart quality score distribution 14
QuanTP Correlation between protein and transcript abundances 2
QuantWiz-IQ Isobaric Quantitation using QuantWiz-IQ 1
Quast Genome assembly Quality 14
Query Tabular using sqlite sql 8
Racon Consensus module for raw de novo DNA assembly of long uncorrected reads 8
RagTag reference-guided scaffolding of draft genomes 2
Ramachandran Analysis - Ramachandran plot for proteins 2
Ramachandran Plots - calculate and plot the distribution of two dihedrals in a trajectory 4
Rank Pathways : Assess the impact of a gene set on KEGG pathways 4
Rank Terms : Assess the enrichment/depletion of a gene set for GO terms 3
Rarefaction.shared Generate inter-sample rarefaction curves for OTUs 5
Rarefaction.single Generate intra-sample rarefaction curves for OTUs 6
Raven De novo assembly of Oxford Nanopore Technologies data 5
Raw Tools Perform scan data parsing, quantification and quality control analysis of Thermo Orbitrap raw mass spectrometer files. 1
RAxML : construct a maximum-likelihood phylogenetic tree 2
RCAS - RNA Centric Annotation System 2
RDConf: Low-energy ligand conformer search using RDKit 1
RDF Analysis - Radial Distribution Function between two atoms 4
rDock cavity definition - generate the active site definition needed for rDock docking 2
rDock docking - perform protein-ligand docking with rDock 6
rDock docking using the sdsort provided with rDock 3
Re-align with SRMA 1
Reaction maker using RDKit 2
Reaction SMARTS filter using RDKit 2
Reactivity Calculation calculates structural reactivity on each nucleotide based on RT stop counts from the Get RT Stop Counts module 1
Read Distribution calculates how mapped reads were distributed over genome feature 12
Read Duplication determines reads duplication rate with sequence-based and mapping-based strategies 10
Read GC determines GC% and read count 10
Read It and Keep 2
Read length statistics from a set of FAST5 files 2
Read NVC to check the nucleotide composition bias 10
Read Quality determines Phred quality score 10
Realign reads with LoFreq viterbi 5
Rebase GFF3 features against parent features 2
Recentrifuge Robust comparative analysis and contamination removal for metagenomics Statistical calculation Taxonomic classification 3
Red repeat masking 2
Reduce a joined HUMAnN table Nucleic acid sequence analysis Phylogenetic analysis 2
Reduce a HUMAnN2 generated table 4
Regex Find And Replace 5
Regex Replace Regular Expression replacement using the Python re module 1
Register Account with Apollo 7
Regroup HUMAnN table features Nucleic acid sequence analysis Phylogenetic analysis 2
Regroup a HUMAnN2 generated table by features 4
Reheader copy SAM/BAM header between datasets 4
RelateObjects assign relationships parent-children between objects 2
Remarkable Intervals : Find high-scoring runs of SNPs 3
Remove 3'-end nts from FASTQ 3
Remove beginning of a file 1
Remove columns by heading 2
Remove confounders with scanpy 7
Remove counterions and fragments from a library of compounds 7
Remove counterions and fragments 2
Remove duplicated molecules from a library of compounds 5
Remove protonation state of every atom 6
Remove sequencing artifacts 5
Remove small molecules from a library of compounds 5
Remove spurious crosslinking events 3
Remove Unwanted Variation from RNA-seq data 4
Remove.dists Removes distances from a phylip or column file 6
Remove.groups Remove groups from groups,fasta,names,list,taxonomy 5
Remove.lineage Picks by taxon 5
Remove.otulabels Removes OTU labels 6
Remove.otus Removes OTUs from various file formats 5
Remove.rare Remove rare OTUs 5
Remove.seqs Remove sequences by name 6
remuRNA Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation 1
Rename features of a HUMAnN2 generated table 4
Rename features of a HUMAnN generated table Nucleic acid sequence analysis Phylogenetic analysis 2
Rename OME-TIFF Channels Change the channel names in the XML metadata of OME-TIFF images 1
Rename sequences 5
Rename.seqs Rename sequences by concatenating the group name 2
Renormalize a HUMAnN generated table Nucleic acid sequence analysis Phylogenetic analysis 3
Renormalize a HUMAnN2 generated table 5
Reorder individuals : exchange rows in the above picture 2
ReorderSam reorder reads to match ordering in reference sequences 17
RepeatMasker screen DNA sequences for interspersed repeats and low complexity regions Repeat sequence analysis 8
RepeatModeler Model repetitive DNA 2
Replace parts of text 12
Replace ambiguous codons in a multiple alignment using HyPhy 4
Replace chromosome names in a tabular dataset using a mapping table 1
Replace column by values which are defined in a convert file 2
Replace Text in a specific column 11
Replace Text in entire line 11
ReplaceSamHeader replace header in a SAM/BAM dataset 17
Replicate Filter - Remove peaks that fail to appear in at least x-out-of-n (technical) replicates 2
Resampling - determine per-gene p-values 5
Resize coordinate window of GFF data 3
Restore Attributes : Fill in missing properties for a gd_snp or gd_genotype dataset 3
Retrieve a run report 2
Retrieve an analysis report 2
Retrieve Data from Apollo into Galaxy 8
Retrieve ENA data (other than taxon and project) 2
Retrieve ENA taxon data 2
Retrieve JBrowse for an organism, from Apollo 8
Reverse columns in a tabular file 5
Reverse Complement a MAF file 1
Reverse-Complement 5
Reverse.seqs Reverse complement the sequences 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 14
revertR2orientationInBam Revert the mapped orientation of R2 mates in a bam. 1
RevertSam revert SAM/BAM datasets to a previous state 14
revseq Reverse and complement a sequence 5
RGCCA performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals. Analysis Correlation Visualisation 2
ribotaper part 1: creation of annotation files 4
ribotaper part 2: metagene analysis for P-sites definition 4
ribotaper part 3: ribosome profiling 4
riboWaltz calculation of optimal P-site offsets and diagnostic analysis Translation initiation site prediction 1
riboWaltz-plot visual inspection of ribosome profiling data Translation initiation site prediction 1
RmDup remove PCR duplicates 5
RMSD Analysis using Bio3D 2
RMSF Analysis using Bio3D 2
RNA fragment size calculates the fragment size for each gene/transcript 8
RNA STAR Gapped-read mapper for RNA-seq data Mapping assembly Sequence alignment 19
RNA STARSolo mapping, demultiplexing and gene quantification for single cell RNA-seq Sequence alignment 8
RNA Structure Prediction predict RNA structures with or without experimental constraints from the Reactivity Calculation module 1
RNA-seq Rcorrector a kmer-based error correction method for RNA-seq data 1
RNA/DNA converter 5
RNA2Dfold explore structure space between two reference structures 1
RNAaliduplex find binding sites of two RNA alignments 1
RNAalifold Calculate minimum free energy secondary structures and partition function on a multiple alignment file 2
RNABOB Fast Pattern searching for RNA secondary structures 2
RNAcode Analyze the protein coding potential in MSA. 3
RNAcofold Calculate secondary structures of two RNAs with dimerization 1
RNAcommender genome-wide recommendation of RNA-protein interactions 2
RNADigestor Digests an RNA sequence database in-silico. 2
RNAdistance Calculate distance between secondary structures of two RNAs 1
RNAduplex Compute the structure upon hybridization of two RNA strands 1
RNAeval Calculate energy of RNA sequences with given secondary structure 1
RNAfold Calculate minimum free energy secondary structures and partition function of RNAs 4
RNAheat Calculate energies of RNA in a temperature range 1
RNAinverse Calculate RNA sequence from secondary structure 1
RNALalifold Calculate locally stable secondary structures for a set of aligned RNAs 1
RNALfold calculates locally stable secondary structures of RNA 1
RNALfoldz calculates locally stable secondary structures of RNA 1
RNAlien Unsupervised covariance model construction from a single input sequence 1
RNAMassCalculator Calculates masses, mass-to-charge ratios and sum formulas of RNA sequences 2
RNApaln RNA alignment based on sequence base pairing propensities 1
RNApdist Calculate distances between thermodynamic RNA secondary structure ensembles 1
RNAPKplex predicts RNA secondary structures including pseudoknots 1
RNAplex Find targets of a query RNA 1
RNAplot Draw RNA Secondary Structures 1
rnaQUAST A Quality Assessment Tool for De Novo Transcriptome Assemblies 3
RNASeq samples quality check for transcript quantification 11
RNAshapes RNA Secondary structure prediction 2
RNAsnoop Find targets of a query H/ACA snoRNA 1
RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs 1
rnaSPAdes de novo transcriptome assembler 13
RNAsubopt Calculates suboptimal secondary structures of RNAs 1
RNAup Calculate the thermodynamics of RNA-RNA interactions 1
rnaviralSPAdes de novo assembler for transcriptomes, metatranscriptomes and metaviromes 6
RNAz predicting structurally conserved and thermodynamically stable RNA secondary structures 3
RNAz Cluster 1
RNAz Randomize Aln 1
RNAz Select Seqs 1
RNAz windows 1
RNPxl Tool for RNP cross linking experiment analysis. 2
RNPxlSearch Annotate RNA to peptide crosslinks in MS/MS spectra. 4
RNPxlXICFilter Remove MS2 spectra from treatment based on the fold change between control and treatment. 5
Roary the pangenome pipeline - Quickly generate a core gene alignment from gff3 files 8
Rolling window over a dataframe (e.g. for data smoothing) 1
RPKM Count calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 4
RPKM Saturation calculates raw count and RPKM values for transcript at exon, intron, and mRNA level 12
RSEM calculate expression RNA-Seq by Expectation-Maximization 1
RSEM prepare reference 1
RSEM trinity fasta to gene map extract transcript to gene map from trinity 1
RTEvaluation Application that evaluates TPs (true positives), TNs, FPs, and FNs for an idXML file with predicted RTs. 5
RTModel Trains a model for the retention time prediction of peptides from a training set. 4
RTPredict Predicts retention times for peptides using a model trained by RTModel. 2
rtsne 1
Run a core set of QIIME diversity analyses (core_diversity_analyses) 2
Run join_paired_ends on multiple files (multiple_join_paired_ends) 2
Run OpenDUck steered molecular dynamics runs 1
Run SCCAF to assess and optimise clustering 2
Run split_libraries_fastq on multiple files (multiple_split_libraries_fastq) 2
rxDock cavity definition - generate the active site definition needed for rxDock docking 3
rxDock docking - perform protein-ligand docking with rxDock 4
RXLR Motifs Find RXLR Effectors of Plant Pathogenic Oomycetes 5
s3segmenter single cell (nuclei and cytoplasm) label masks. 1
Sailfish transcript quantification from RNA-seq data 4
Salmon quant Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads 13
Salmon quantmerge Merge multiple quantification results into a single file 5
Salmonella Subtyping 2
salmonKallistoMtxTo10x Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data 3
SALSA scaffold long read assemblies with Hi-C 5
sam-to-bam converter 1
sam-to-bigwig converter 1
sam-to-qname_sorted.bam converter 1
sam-to-unsorted.bam converter 1
SAM/BAM Alignment Summary Metrics 2
SampComp to compare Nanopolished datasets 2
Sample Filter Remove peaks that fail to appear in x-out-of-n (biological) samples 2
Sample SNPs : Select a specified number of SNPs, uniformly spaced 2
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 19
Samtools ampliconclip clip primer bases from bam files 2
samtools BAM to CRAM convert BAM alignments to CRAM format 4
Samtools calmd recalculate MD/NM tags 4
Samtools coverage computes the depth at each position or region 2
Samtools depth compute the depth at each position or region 4
Samtools fastx extract FASTA or FASTQ from alignment files 3
Samtools fixmate fill mate coordinates, ISIZE and mate related flags 3
Samtools flagstat tabulate descriptive stats for BAM datset 8
Samtools markdup marks duplicate alignments 7
Samtools merge merge multiple sorted alignment files 3
samtools mpileup multi-way pileup of variants 11
Samtools sort order of storing aligned sequences 7
Samtools split BAM dataset on readgroups 5
Samtools stats generate statistics for BAM dataset 7
Samtools view - reformat, filter, or subsample SAM, BAM or CRAM 9
sansa annotate structural variants Genetic variation analysis 2
sarscov2formatter 3
sarscov2summary 1
SaveImages or movie files 2
SC3 Calculate Consensus from multiple runs of k-means clustering 1
SC3 Calculate Distances between cells 1
SC3 Calculate Transformations of distances using PCA and graph Laplacian 1
SC3 DiffExp calculates DE genes, marker genes and cell outliers 1
SC3 Estimate the number of clusters for k-means clustering 1
SC3 K-Means perform k-means clustering 1
SC3 Prepare a sc3 SingleCellExperiment object 1
Scale Image Scales image 3
scanMotifGenomeWide 1
Scanpy BBKNN batch-balanced K-nearest neighbours 6
Scanpy ComBat adjust expression for variables that might introduce batch effect 6
Scanpy ComputeGraph to derive kNN graph 16
Scanpy DiffusionMap calculate diffusion components 11
Scanpy DPT diffusion pseudotime inference 11
Scanpy FilterCells based on counts and numbers of genes expressed 15
Scanpy FilterGenes based on counts and numbers of cells expressed 15
Scanpy FindCluster based on community detection on KNN graph 17
Scanpy FindMarkers to find differentially expressed genes between groups 17
Scanpy FindVariableGenes based on normalised dispersion of expression 13
Scanpy Harmony adjust principal components for variables that might introduce batch effect 7
Scanpy MNN correct batch effects by matching mutual nearest neighbors 6
Scanpy NormaliseData to make all cells having the same total expression 14
Scanpy PAGA trajectory inference 10
Scanpy ParameterIterator produce an iteration over a defined parameter 5
Scanpy Plot Scrublet visualise multiplet scoring distribution 2
Scanpy PlotEmbed visualise cell embeddings 12
Scanpy PlotTrajectory visualise cell trajectories 11
Scanpy Read10x into hdf5 object handled by scanpy 13
Scanpy RegressOut variables that might introduce batch effect 10
Scanpy RunFDG visualise cell clusters using force-directed graph 11
Scanpy RunPCA for dimensionality reduction 14
Scanpy RunTSNE visualise cell clusters using tSNE 15
Scanpy RunUMAP visualise cell clusters using UMAP 14
Scanpy ScaleData to make expression variance the same for all genes 13
Scanpy Scrublet remove multiplets from annData objects with Scrublet 2
Scater CalculateCPM from raw counts 1
Scater CalculateQcMetrics based on expression values and experiment information 1
Scater DetectOutlier cells based on expression metrics 1
Scater read 10x data Loads 10x data into a serialized scater R object 1
Scater: Calculate QC metrics Computes QC metrics from single-cell expression matrix 4
Scater: filter SCE with user-defined parameters or PCA 5
Scater: normalize SCE Compute normalised expression values for SCE 3
Scater: PCA plot cell-level reduced dimension of a normalised SCE 4
Scater: plot expression frequency Plot the frequency of expression against the mean expression level for SCE 2
Scater: plot library QC to visualise library size, feature counts and mito gene expression 4
Scater: t-SNE plot Produces a t-SNE plot of two components 3
Scatterplot of two numeric columns 4
Scatterplot with ggplot2 10
SCCAF Assesment runs an assesment of an SCCAF optimisation result or an existing clustering. 2
SCCAF Assesment Merger brings together distributed assesments. 2
SCCAF mulitple regress out with multiple categorical keys on an AnnData object. 1
SCEasy convert a data object between formats 1
scHicAdjustMatrix clusters single-cell Hi-C interaction matrices on the raw data 2
scHicCluster clusters single-cell Hi-C interaction matrices on the raw data 2
scHicClusterCompartments clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction 2
scHicClusterMinHash clusters single-cell Hi-C interaction matrices with MinHash dimension reduction 2
scHicClusterSVL clusters single-cell Hi-C interaction matrices with svl dimension reduction 2
scHicConsensusMatrices creates per cluster one average matrix 2
scHicCorrectMatrices correct with KR algorithm single-cell Hi-C interaction matrices 2
scHicCreateBulkMatrix creates the bulk matrix out of single-cell Hi-C interaction matrices 1
scHicDemultiplex demultiplexes Nagano 2017 raw fastq files 2
scHicInfo information about a single-cell scool matrix 2
scHicMergeMatrixBins change the resolution of the scHi-C matrices 2
scHicMergeToSCool merge multiple cool files to one scool file 1
scHicNormalize normalize single-cell Hi-C interaction matrices to the same read coverage 2
scHicPlotClusterProfiles plot single-cell Hi-C interaction matrices cluster profiles 2
scHicPlotConsensusMatrices plot single-cell Hi-C interaction matrices cluster consensus matrices 2
scHicQualityControl quality control for single-cell Hi-C interaction matrices 2
Scmap cell projection searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets. 6
Scmap cluster projection projects one dataset to another 5
Scmap get standard output Create final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package 3
Scmap index cells creates a cell index for a dataset to enable fast approximate nearest neighbour search 7
Scmap index clusters calculates centroids of each cell type and merges them into a single table 6
Scmap pre-process Pre-process SCE object before running downstream analysis 2
Scmap select features finds the most informative features (genes/transcripts) for projection. 5
Scoary calculates the assocations between all genes in the accessory genome and the traits 1
Score docked poses using SuCOS - compare shape and feature overlap of docked ligand poses to a reference molecule 4
scPipe - preprocessing pipeline for single cell RNA-seq 4
Scpred - get output in standard format This method allows to export predicted labels in a standardised format, simplifying downstream analyses. 4
Scpred eigen-decompose Perform matrix eigen-decomposition; initialize object of scPred class 3
ScPred feature space Get feature space for training matrix 4
Scpred pre-process Pre-process input dataset (no train/test split) 1
Scpred predict Make cell type predictions using trained model. 4
Scpred train Train classification model 4
Scpred train-test split CPM normalise and partition into train/test data 3
scran_normalize Normalize raw counts expression values using deconvolution size factors 1
Screen a compound against a library using RDKit 2
Screen.seqs Screen sequences 6
SDF sort and filter using the sdsort provided with rxDock 3
SDF to Fingerprint - extract fingerprints from sdf file metadata 5
SEACR for sparse enrichment analysis 1
Search ChEMBL database for compounds which are similar to a SMILES string 6
Search ENA data given a query 2
Search engine output to Pin converter to create Percolator input files 2
Search GUI Perform protein identification using various search engines and prepare results for input to Peptide Shaker 22
Search in textfiles (grep) 11
SearchToLib Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data 3
Secure Hash / Message Digest on a dataset 2
SeedListGenerator Generates seed lists for feature detection. 3
segemehl short read mapping with gaps 3
segmentation-fold RNA-Folding including predefined segments including K-turns 4
SegMetrics image segmentation and object detection performance measures 1
Select lines that match an expression Filtering 3
Select first lines from a dataset Filtering 4
Select first lines from a dataset (head) 9
Select high quality segments 2
Select last lines from a dataset 2
Select last lines from a dataset (tail) 9
Select random lines from a file 2
Select Sequences Tool to select representative sequences from a multiple sequence alignment. 2
SemanticValidator SemanticValidator for semantically validating certain XML files. 4
SemiBin for Semi-supervised Metagenomic Binning 1
SemiBin: Concatenate fasta files for multi-sample binning 1
SemiBin: Contig annotations 1
SemiBin: Generate sequence features (kmer and abundance) as training data for semi-supervised deep learning model training 1
SemiBin: Group the contigs into bins 1
SemiBin: Train the semi-supervised deep learning model 1
Send to cloud 1
Sens.spec Determine the quality of OTU assignment 6
Separate pgSnp alleles into columns 1
Seq.error assess error rates in sequencing data 5
seq2HLA HLA genotype and expression from RNA-seq 2
SeqKit fx2tab convert FASTA/Q to tabular 3
SeqKit locate subsequences/motifs, mismatch allowed 2
SeqKit statistics of FASTA/Q files 3
seqmatchall All-against-all comparison of a set of sequences 5
seqret Reads and writes sequences 5
seqtk_comp get the nucleotide composition of FASTA/Q 6
seqtk_cutN cut sequence at long N 6
seqtk_dropse drop unpaired from interleaved Paired End FASTA/Q 6
seqtk_fqchk fastq QC (base/quality summary) 6
seqtk_hety regional heterozygosity 6
seqtk_listhet extract the position of each het 6
seqtk_mergefa merge two FASTA/Q files 6
seqtk_mergepe interleave two unpaired FASTA/Q files for a paired-end file 6
seqtk_mutfa point mutate FASTA at specified positions 6
seqtk_randbase choose a random base from hets 6
seqtk_sample random subsample of fasta or fastq sequences 6
seqtk_seq common transformation of FASTA/Q 6
seqtk_subseq extract subsequences from FASTA/Q files 6
seqtk_trimfq trim FASTQ using the Phred algorithm 6
Sequence composition Count bases or amino-acids 3
Sequence converter for various sequence formats 1
Sequence Logo generator for fasta (eg Clustal alignments) 2
SequenceCoverageCalculator Prints information about idXML files. 5
seqwish Alignment to variation graph inducer 7
Seurat - toolkit for exploration of single-cell RNA-seq data 12
Seurat CreateSeuratObject create a Seurat object 1
Seurat Export2CellBrowser produces files for UCSC CellBrowser import. 5
Seurat FilterCells filter cells in a Seurat object 5
Seurat FindClusters find clusters of cells 5
Seurat FindMarkers find markers (differentially expressed genes) 5
Seurat FindNeighbours constructs a Shared Nearest Neighbor (SNN) Graph 4
Seurat FindVariableGenes identify variable genes 5
Seurat NormaliseData normalise data 5
Seurat Plot dimension reduction graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class. 5
Seurat Read10x Loads Tabular or 10x data into a serialized seurat R object 5
Seurat RunPCA run a PCA dimensionality reduction 5
Seurat RunTSNE run t-SNE dimensionality reduction 5
Seurat ScaleData scale and center genes 5
SFF converter 1
Sffinfo Summarize the quality of sequences 5
Sharpen 2
Shasta De novo assembly of long read sequencing data 1
Shhh.flows Denoise flowgrams (PyroNoise algorithm) 5
Shhh.seqs Denoise program (Quince SeqNoise) 5
shift longitudes from netCDF data 1
Shovill Faster SPAdes assembly of Illumina reads 8
Show nucleotide distribution in nanopore sequencing reads 2
Show quality score distribution in nanopore sequencing reads 2
Show-Coords Parse delta file and report coordinates and other information Read mapping Sequence alignment 5
showfeat Show features of a sequence 5
shuffleseq Shuffles a set of sequences maintaining composition 5
SICER Statistical approach for the Identification of ChIP-Enriched Regions 3
Sickle windowed adaptive trimming of FASTQ data 4
SIFT predictions of functional sites 1
sigcleave Reports protein signal cleavage sites 5
SignalP 3.0 Find signal peptides in protein sequences 4
Similarity search of fingerprint data sets with chemfp 4
SimpleSearchEngine Annotates MS/MS spectra using SimpleSearchEngine. 4
SINA reference based multiple sequence alignment 5
SIRIUS-CSI:FingerID is used to identify metabolites using single and tandem mass spectrometry 7
SiriusAdapter Tool for metabolite identification using single and tandem mass spectrometry 4
sirna Finds siRNA duplexes in mRNA 5
sistr_cmd Salmonella In Silico Typing Resource commandline tool for serovar prediction 3
sixgill build a metapeptide database from metagenome fastq files 1
sixgill filter a metapeptide database 1
sixgill makefasta from a metapeptide database 1
sixgill merge metapeptide databases 1
sixpack Display a DNA sequence with 6-frame translation and ORFs 7
Skeletonize 2
skipseq Reads and writes sequences, skipping first few 5
Slamdunk - streamlining SLAM-seq analysis with ultra-high sensitivity 6
Slice BAM by genomic regions 5
Slice Image into smaller patches 2
Slice MD trajectories using the MDTraj package 3
Slice VCF to get data from selected regions 1
smi-to-mol converter 2
smi-to-smi converter 2
smina Scoring and Minimization with AutoDock Vina 1
Smooth 2
Smudgeplot inference of ploidy and heterozygosity structure using whole genome sequencing 1
sniffles Structural variation caller using third generation sequencing 1
snipit Summarise snps relative to a reference sequence 2
snippy Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. 11
snippy-clean_full_aln Replace any non-standard sequence characters in snippy 'core.full.aln' file. 4
snippy-core Combine multiple Snippy outputs into a core SNP alignment 10
SNP distance matrix Compute distance in SNPs between all sequences in a FASTA file 2
SnpEff build: database from Genbank or GFF record 13
SnpEff chromosome-info: list chromosome names/lengths 8
SnpEff databases: list available databases 13
SnpEff download: download a pre-built database 13
SnpEff eff: annotate variants 11
SnpEff eff: annotate variants for SARS-CoV-2 1
SnpEff Ensembl CDS Report Variant coding sequence changes for SnpEffects 1
SnpEff to Peptide fasta to create a Search DB fasta for variant SAP peptides 1
snpFreq significant SNPs in case-control data 2
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift dbNSFP Add Annotations from dbNSFP and similar annotation DBs 2
SnpSift dbNSFP Add annotations from dbNSFP or similar annotation DBs 4
SnpSift Extract Fields from a VCF file into a tabular file 7
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift GeneSets Annotating GeneSets, such as Gene Ontology, KEGG, Reactome 4
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 8
SnpSift Variant Type Annotate with variant type 8
SnpSift vcfCheck basic checks for VCF specification compliance 8
socru Calculate the order and orientation of complete bacterial genomes 1
SOPRA with prebuilt contigs for Illumina libraries 1
Sort data in ascending or descending order Sorting 3
Sort data in ascending or descending order 11
Sort a row according to their columns 12
Sort assembly 5
Sort Column Order by heading 1
Sort.seqs put sequences in different files in the same order 6
SortSam sort SAM/BAM dataset 14
SPAdes genome assembler for genomes of regular and single-cell projects Genome assembly 16
Spaln: align cDNA or Protein to genome Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 5
Sparse Matrix Functions for manipulating 2-D Scipy sparse numeric data 11
Spatial coordinates anonymization without loss of the spatial relationships 1
Species tree generator from a list of species using the ETE Toolkit 1
Specify Individuals : Define a collection of individuals from a gd_snp dataset 3
SpecLibCreator Creates an MSP formatted spectral library. 4
SpecLibSearcher Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library. 3
SpectraFilterBernNorm Applies thresholdfilter to peak spectra. 4
SpectraFilterMarkerMower Applies thresholdfilter to peak spectra. 4
SpectraFilterNLargest Applies thresholdfilter to peak spectra. 5
SpectraFilterNormalizer Normalizes intensity of peak spectra. 5
SpectraFilterParentPeakMower Applies thresholdfilter to peak spectra. 4
SpectraFilterScaler Applies thresholdfilter to peak spectra. 4
SpectraFilterSqrtMower Applies thresholdfilter to peak spectra. 4
SpectraFilterThresholdMower Applies thresholdfilter to peak spectra. 5
SpectraFilterWindowMower Applies thresholdfilter to peak spectra. 4
SpectraMerger Merges spectra (each MS level separately), increasing S/N ratios. 5
SpectraSTSearchAdapter Interface to the SEARCH Mode of the SpectraST executable 4
Spectrophores search - similarity search based on 1D chemical features 5
Spectrophores(TM) search: similarity search based on 1D chemical features 2
Split a merged HUMAnN table Nucleic acid sequence analysis Phylogenetic analysis 2
Split a HUMAnN2 generated table 4
Split a HUMAnN table into 2 tables (one stratified and one unstratified) Nucleic acid sequence analysis Phylogenetic analysis 3
Split BAM by Mapped 2
Split BAM by Paired/Single End 2
Split BAM by Reference into dataset list collection 2
Split BAM by Tag into dataset list collection 2
Split Dataset into training and test subsets 6
Split Fasta files into a collection 3
Split fastq libraries to performs demultiplexing of Fastq sequence data (split_libraries_fastq) 2
Split file according to the values of a column 4
Split file to dataset collection 7
Split Labelmap 1
Split libraries according to barcodes specified in mapping file (split_libraries) 2
Split MAF blocks by Species 1
Split objects Split binary image by using watershed 1
Split stratified table 3
Split.abund Separate sequences into rare and abundant groups 5
Split.groups Generates a fasta file for each group 5
splitter Split a sequence into (overlapping) smaller sequences 5
Spot Detection in a 2D image (sequence) 3
SpoTyping fast and accurate in silico Mycobacterium spoligotyping from sequence reads 1
SPRING Cross reference builder 1
SPRING Map with BLAST 1
SPRING MCC plot generator 1
SPRING Min-Z filter operation 1
SPRING Model complex structures 1
SPRING Model-All complex structures 1
SpyBOAT wavelet analyzes image stacks 2
SQLite to tabular for SQL query 3
Squidpy Graph and Plotting for spatial analysis 1
sRNAPipe In-depth study of small RNA 4
SRST2 Short Read Sequence Typing for Bacterial Pathogens 2
SSAKE short DNA sequences assembler 1
ssHMM - RNA sequence-structure motif finder 1
Stacking Ensembles builds stacking, voting ensemble models with numerous base options 8
Stacks2: clone filter Identify PCR clones 8
Stacks2: cstacks Generate catalog of loci 8
Stacks2: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 8
Stacks2: gstacks Call variants, genotypes and haplotype 8
Stacks2: kmer filter Identify PCR clones 8
Stacks2: populations Calculate population-level summary statistics 8
Stacks2: process radtags the Stacks demultiplexing script 8
Stacks2: process shortreads fast cleaning of randomly sheared genomic or transcriptomic data 8
Stacks2: reference map the Stacks pipeline with a reference genome (ref_map.pl) 8
Stacks2: sstacks Match samples to the catalog 8
Stacks2: tsv2bam Sort reads by RAD locus 8
Stacks2: ustacks Identify unique stacks 8
Stacks: assemble read pairs by locus run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers 6
Stacks: clone filter Identify PCR clones 2
Stacks: cstacks build a catalogue of loci 5
Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) 5
Stacks: genotypes analyse haplotypes or genotypes in a genetic cross ('genotypes' program) 5
Stacks: populations analyze a population of individual samples ('populations' program) 5
Stacks: process radtags the Stacks demultiplexing script 5
Stacks: pstacks find stacks from short reads mapped to a reference genome 5
Stacks: reference map the Stacks pipeline with a reference genome (ref_map.pl) 5
Stacks: rxstacks make corrections to genotype and haplotype calls 5
Stacks: sstacks match stacks to a catalog 4
Stacks: statistics on stacks found for multiple samples 2
Stacks: ustacks align short reads into stacks 5
Standardize SD-files using RDKit 2
STAR-Fusion detect fusion genes in RNA-Seq data 4
staramr Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes. 11
Starting Modules load images and metadata into CellProfiler (Images, Metadata, NamesAndTypes, Groups) 2
Statistical hypothesis testing computes several descriptive statistics 1
Statistics on presence-absence of a numeric variable 1
Stitch Gene blocks given a set of coding exon intervals 4
Stitch MAF blocks given a set of genomic intervals 1
Strelka Germline small variant caller for germline variation in small cohorts 2
Strelka Somatic small variant caller for somatic variation in tumor/normal sample pairs 1
StringTie transcript assembly and quantification 17
StringTie merge transcripts 11
Structure using multi-locus genotype data to investigate population structure 2
Structure to GSPAN 3
Sub-sample sequences files e.g. to reduce coverage 4
Sub.sample Create a sub sample 5
Subset columns from a VCF dataset 1
Substructure Search of fingerprint data sets 2
Substructure Search of fingerprint data sets 5
Subtract the intervals of two datasets Filtering 6
Subtract Whole Dataset from another dataset 2
Summarize taxa and store results in a new table or appended to an existing mapping file (summarize_taxa) 2
Summarize taxonomy 1
Summary Statistics for any numerical column 3
Summary.qual Summarize the quality scores 6
Summary.seqs Summarize the quality of sequences 5
Summary.shared Summary of calculator values for OTUs 5
Summary.single Summary of calculator values for OTUs 6
Summary.tax Assign sequences to taxonomy 5
supermatcher Match large sequences against one or more other sequences 5
Support vector machines (SVMs) for classification 2
Support vector machines (SVMs) for classification 12
SvmTheoreticalSpectrumGeneratorTrainer Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator 5
Switch axis coordinates Switches the axes of an image and flips the y axis. 1
syco Synonymous codon usage Gribskov statistic plot 5
syndiva diversity analysis of synthetic libraries of a Fibronectin domain 1
T Test for Two Samples 2
T-Coffee multiple sequence alignment 3
Table Compute computes operations on table data 4
Table Merge Merging dataMatrix with a metadata table 2
Table to GFF3 2
Tabular to FASTQ converter Conversion 5
tabular-to-csv converter 1
Tabular-to-FASTA converts tabular file to FASTA format 2
tac reverse a file (reverse cat) 9
Tadarida data cleaner clean data from animal detection on acoustic recordings 1
Tadarida identifications validation Integrate identifications from animal detection on acoustic recordings 1
Tag pileup frequency 3
tar-to-directory converter 2
TargetedFileConverter Converts different transition files for targeted proteomics / metabolomics analysis. 4
TargetFinder plant small RNA target prediction tool Sequence alignment 2
Taxonomy-to-Krona convert a mothur taxonomy file to Krona input format 2
Taylor-Butina clustering of molecular fingerprints 5
TB Variant Filter M. tuberculosis H37Rv VCF filter 4
TB Variant Report - generate HTML report from SnpEff annotated M.tb VCF(s) 3
TB-Profiler Profile Infer strain types and drug resistance markers from sequences 15
tcode Fickett TESTCODE statistic to identify protein-coding DNA 5
TEfinder Transposable element insertions finder 2
Temporal trend indicator using GlmmTMB or GAM models 2
TEtranscripts annotates reads to genes and transposable elements 4
TETyper Transposable Element Typer 3
Text reformatting with awk 13
Text to wordmatrix by extracting most frequent words 1
Text transformation with sed 11
TextExporter Exports various XML formats to a text file. 4
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
TGS-GapCloser fills the N-gap of error-prone long reads 1
Thermo RAW file converter 9
Thread nucleotides onto a protein alignment (back-translation) Gives a codon aware alignment 5
TICCalculator Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). 4
Tile tiles images together to form large montage images 2
tmap Displays membrane spanning regions 5
TMHMM 2.0 Find transmembrane domains in protein sequences 5
Tn5Gaps - determine essential genes 3
TN93 compute distances between aligned sequences 3
TN93 Cluster sequences that lie within a specific distance of each other 2
TN93 Filter - remove sequences from a reference that are within a given distance of of a cluster 2
To categorical Converts a class vector (integers) to binary class matrix 2
TOFCalibration Applies time of flight calibration. 4
Tombo create browser text output 1
Tombo detect modifications detecting shifts in raw current signal level, indicative of non-canonical bases 1
Tombo plot genome locations Plotting amperage signal from nanopore reads at the locations specified 1
Tombo plot most signficant Plotting amperage signal at the locations deemed most significant by the tombo 1
Tombo Re-squiggle Raw Signal (electric current nanopore measurements) Genomic Alignment 1
TopHat Gapped-read mapper for RNA-seq data 9
Tophat Fusion Post post-processing to identify fusion genes 2
TopPerc Facilitate input to Percolator and reintegrate. 2
TrackObjects tracking objects throughout sequential frames of a series of images 2
tracy Align chromatogram to a FASTA reference 1
tracy Assemble genomic region from tiled, overlapping Sanger Chromatogram trace files 1
tracy Basecall from Sanger chromatogram tracefile 1
tracy Decompose heterozygous mutations (and call variants) 1
Train a CheRRI model using RRIs 2
Train Augustus ab-initio gene predictor 5
Train SNAP ab-initio gene predictor 1
Train, Test and Evaluation fit a model using part of dataset and evaluate using the rest 7
Trajectory select and merge - select specific molecules and merge multiple trajectories. 3
tranalign Align nucleic coding regions given the aligned proteins 5
Transcript Integrity Number evaluates RNA integrity at a transcript level 8
TransDecoder finds coding regions within transcripts 7
transeq Translate nucleic acid sequences 5
Transform real vector graphs to sparse vectors 1
Transformation Transforms the dataMatrix intensity values 1
TransformationEvaluation Applies a transformation to a range of values 4
Translate BED Sequences 3 frame translation of BED augmented with a sequence column 1
Translate BED transcripts cDNA in 3frames or CDS 1
Translate nucleotides to amino acids 1
Transpose rows/columns in a tabular file 5
TransTermHP finds rho-independent transcription terminators in bacterial genomes 2
Tree.shared Generate a newick tree for dissimilarity among groups 5
TreeBeST best Generate a phylogenetic tree using CDS alignment and species tree 2
TreeBeST best Generate a phylogenetic tree using CDS alignment and species tree 1
TRIC integrates information from all available runs via a graph-based alignment strategy 1
Trim leading or trailing characters 2
Trim Galore! Quality and adapter trimmer of reads 9
Trim putative adapter sequence 1
Trim sequences 5
Trim.flows partition by barcode, trim to length, cull by length and mismatches 5
Trim.seqs Trim sequences - primers, barcodes, quality 5
trimest Trim poly-A tails off EST sequences 5
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 15
TrimN 1
trimseq Trim ambiguous bits off the ends of sequences 5
Trinity de novo assembly of RNA-Seq data 14
Trinotate functional transcript annotation 4
tRNA and tmRNA prediction (Aragorn) 3
tRNA prediction (tRNAscan) 2
Trycycler cluster cluster the contigs of your input assemblies into per-replicon groups Genome assembly 4
Trycycler consensus generate a consensus contig sequence for each cluster Genome assembly 4
Trycycler partition assign the reads to the clusters Genome assembly 4
Trycycler reconcile/msa reconcile the contigs within each cluster and perform a multiple sequence alignment Genome assembly 4
Trycycler subsample make a maximally-independent read subsets of an appropiate depth for your genome Genome assembly 4
twoBitToFa Convert all or part of .2bit file to FASTA 3
twofeat Finds neighbouring pairs of features in sequences 5
tximport Summarize transcript-level estimates for gene-level analysis 3
UCSC Cell Browser displays single-cell clusterized data in an interactive web application. 5
UMI-tools count performs quantification of UMIs from BAM files 9
UMI-tools deduplicate Extract UMI from fastq files 6
UMI-tools extract Extract UMI from fastq files 12
UMI-tools group Extract UMI from fastq files 8
UMI-tools whitelist Extract cell barcodes from FASTQ files 8
UNetCoreograph TMA core detection and dearraying 1
Unfold columns from a table 11
unifrac.unweighted Describes whether two or more communities have the same structure 5
unifrac.weighted Describes whether two or more communities have the same structure 5
union Reads sequence fragments and builds one sequence 5
Unipept retrieve taxonomy for peptides 6
UniProt download proteome as XML or fasta 6
UniProt ID mapping and retrieval 4
Unique occurrences of each record 9
Unique occurrences of each record 1
Unique lines assuming sorted input file 11
Unique.seqs Return unique sequences 5
Univariate Univariate statistics 2
UnMicst Image segmentation - probability map generation 1
Unpack pathway abundances to show the genes for each Nucleic acid sequence analysis Phylogenetic analysis 3
Unpack pathway abundances to show genes included 3
unsorted.bam-to-bigwig converter 1
Unzip Unzip file 1
Upload File from your computer Query and retrieval 3
UpSet diagram of intersection of genomic regions or list sets 4
UShER ultrafast sample placement on existing trees Phylogenetic inference (from molecular sequences) 1
UShER matUtils analyze, edit, and manipulate mutation annotated tree files Phylogenetic inference (from molecular sequences) 1
VALET to detect mis-assemblies in metagenomic assemblies 1
Validate FASTA Database 1
Validate ISO 19139 metadata documents 1
ValidateSamFile assess validity of SAM/BAM dataset 15
VAPOR Classify Influenza samples from short reads sequence data 4
VarDict calls SNVs and indels for tumor-normal pairs 4
Variables exploration Shows interaction, correlation, colinearity, produces a PCA and computes VIF for biodiversity abundance data 1
Variant Annotator process variant counts 3
Variant Frequency Plot Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data Aggregation 4
VarScan for variant detection 2
VarScan copynumber Determine relative tumor copy number from tumor-normal pileups 4
VarScan mpileup for variant detection 4
VarScan somatic Call germline/somatic and LOH variants from tumor-normal sample pairs 9
VCF to MAF Custom Track for display at UCSC 2
VCF to pgSnp Convert from VCF to pgSnp format 1
VCF-BEDintersect: Intersect VCF and BED datasets 5
vcf-to-bgzip converter 2
vcf-to-bigwig converter 1
vcf-to-tabix converter 2
VCF-VCFintersect: Intersect two VCF datasets 5
vcf_bgzip-to-tabix converter 2
VCFaddinfo: Adds info fields from the second dataset which are not present in the first dataset 5
VcfAllelicPrimitives: Split alleleic primitives (gaps or mismatches) into multiple VCF lines 5
vcfanno VCF annotation 2
VCFannotate: Intersect VCF records with BED annotations 5
VCFannotateGenotypes: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset 5
VCFbreakCreateMulti: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 5
VCFcheck: Verify that the reference allele matches the reference genome 5
VCFcombine: Combine multiple VCF datasets 6
VCFcommonSamples: Output records belonging to samples common between two datasets 5
VCFdistance: Calculate distance to the nearest variant 5
VCFfilter: filter VCF data in a variety of attributes 8
VCFfixup: Count the allele frequencies across alleles present in each record in the VCF file 5
VCFflatten: Removes multi-allelic sites by picking the most common alternate 5
VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles 5
VCFgenotypes: Convert numerical representation of genotypes to allelic 5
VCFhetHomAlleles: Count the number of heterozygotes and alleles, compute het/hom ratio 5
VCFleftAlign: Left-align indels and complex variants in VCF dataset 5
VCFprimers: Extract flanking sequences for each VCF record 5
VCFrandomSample: Randomly sample sites from VCF dataset 5
VCFselectsamples: Select samples from a VCF dataset 5
VCFsort: Sort VCF dataset by coordinate 6
VCFtoTab-delimited: Convert VCF data into TAB-delimited format 6
vectorstrip Strips out DNA between a pair of vector sequences 5
Vegan Diversity index 3
Vegan Fisher Alpha index 3
Vegan Rarefaction curve and statistics 3
velvetg Velvet sequence assembler for very short reads De-novo assembly Formatting 6
velveth Prepare a dataset for the Velvet velvetg Assembler De-novo assembly Formatting 6
VelvetOptimiser Automatically optimize Velvet assemblies 5
Venn Generate Venn diagrams for groups 5
Venn Diagram from lists 6
vg convert 1
vg deconstruct construct a dynamic succinct variation graph 2
vg view 2
VINA Docking tool to perform protein-ligand docking with Autodock Vina 5
Violin plot w ggplot2 8
virhunter Deep learning method to identify viruses in sequencing datasets 4
Visceral Evaluate Segmentation 1
Visualisation of compounds 5
Visualize the optimal scoring subnetwork 2
Visualize with Krona Visualise any hierarchical data 1
Vitessce Visualization integrative visualization of multi-modal, spatial single-cell data 1
Volcano Plot create a volcano plot Visualisation 5
VSearch alignment Chimera detection Sequence clustering Sequence masking 6
VSearch chimera detection Chimera detection Sequence clustering Sequence masking 6
VSearch clustering Chimera detection Sequence clustering Sequence masking 7
VSearch dereplication Chimera detection Sequence clustering Sequence masking 7
VSearch masking Chimera detection Sequence clustering Sequence masking 6
VSearch search Chimera detection Sequence clustering Sequence masking 6
VSearch shuffling Chimera detection Sequence clustering Sequence masking 6
VSearch sorting Chimera detection Sequence clustering Sequence masking 7
VT normalize normalizes variants in a VCF file 1
W4m Data Subset Filter W4m data by values or metadata 9
Walnut PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data 3
water Smith-Waterman local alignment 5
Watershed segmentation of binary image 2
Wavelet variance using Discrete Wavelet Transfoms 3
wig-to-bigwig converter 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2
Winnowmap a mapping tool optimized for repetitive sequences Sequence alignment 3
wobble Wobble base plot 5
WoLF PSORT Eukaryote protein subcellular localization prediction 4
wordcount Counts words of a specified size in a DNA sequence 5
wordmatch Finds all exact matches of a given size between 2 sequences 5
WTDBG De novo assembler AND consensuser for long noisy sequences 3
X!Tandem MSMS Search Run an X!Tandem Search 2
X!Tandem MSMS Search Run an X!Tandem Search - test 1
XChem TransFS pose scoring using deep learning 3
xcms adjustRtime (retcor) Retention Time Correction 7
xcms fillChromPeaks (fillPeaks) Integrate areas of missing peaks 7
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 8
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 5
xcms get a sampleMetadata file which need to be filled with extra information 3
xcms groupChromPeaks (group) Perform the correspondence, the grouping of chromatographic peaks within and between samples. 8
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 5
xcms process history Create a summary of XCMS analysis 8
xcms refineChromPeaks (refine) Remove or merge chromatographic peaks based on specific criteria. 1
XCos scoring 2
XFDR Calculates false discovery rate estimates on crosslink identifications 2
xmlstarlet convert a metadata XML file in one standard to another 1
XMLValidator Validates XML files against an XSD schema. 4
XPath compute xpath expressions on XML data 2
XTandemAdapter Annotates MS/MS spectra using X! Tandem. 5
xtc-to-dcd converter 1
YAHS yet another HI-C scaffolding tool 4
zerone 1
zonal statistics over each area 1