European Galaxy tools (3226 and counting)

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Get Data

Faster Download and Extract Reads in FASTQ Download and Extract Reads in FASTQ Download and Extract Reads in BAM IEDB Protein Database Downloader NCBI Accession Download Download and Generate Pileup Format UniProt Get species occurrences data Unipept NCBI ESearch pysradb search NCBI EGQuery NCBI ECitMatch NCBI EPost NCBI ELink NCBI EInfo NCBI ESummary NCBI EFetch UniProt Get sequences by Ensembl ID Get gene tree by Ensembl ID Get features by Ensembl ID Search ENA data Retrieve ENA data Retrieve ENA taxon data Retrieve an analysis report Retrieve a run report EBI Search DoRiNA Search Download run data EGA Download Client Upload File SEEK test NCBI Datasets Genomes NCBI Datasets Gene UCSC Main UCSC Archaea NCBI Datasets Genomes downloads EBI SRA SRA Get Microbial Data BioMart BioMart CBI Rice Mart GrameneMart modENCODE fly InterMine Flymine modENCODE modMine MouseMine Ratmine YeastMine metabolicMine modENCODE worm WormBase ZebrafishMine EuPathDB HbVar OmicsDI

Send Data

ENA Upload tool cURL Send to cloud Export datasets

Collection Operations

Split file Split file Collapse Collection Unzip Extract element identifiers Column join Duplicate file to collection Unzip collection Zip collections Filter failed datasets Filter empty datasets Flatten collection Merge collections Relabel identifiers Filter collection Sort collection Tag elements Apply rules Build list Extract dataset

Expression Tools

Compose text parameter value Calculate numeric parameter value Map parameter value Parse parameter value

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General Text Tools

Text Manipulation

Filter Tabular Histogram Compute diff Replace column Add line to file Add input name as column Merge Columns Switch axis coordinates Table Compute Column Regex Find And Replace Regex Find And Replace Join two files Replace Query Tabular Replace chromosome names SQLite to tabular Replace Text JQ cast Replace Text melt Base Coverage Subtract Text reformatting PRINSEQ Cluster Rebase GFF3 features Remove columns Sort Column Order Join tac Concatenate datasets Multi-Join Unique lines Advanced Cut Select last Sort a row Sort Search in textfiles Unfold Text transformation Create text file Select first Unique Coverage Regex Replace Arithmetic Operations Merge Intersect Fetch closest non-overlapping feature Get flanks Complement Subtract Whole Dataset Unique Add column Split by group Concatenate multiple datasets Add column Concatenate datasets Cut Convert Create single interval Change Case Paste Remove beginning Select random lines Select first Select last Trim Line/Word/Character count Secure Hash / Message Digest

Convert Formats

Convert a 10X BAM file to FASTQ Convert Glimmer to GFF BED-to-GFF GFF-to-BED MAF to BED MAF to Interval MAF to FASTA SFF converter Wig/BedGraph-to-bigWig BED-to-bigBed

Filter and Sort

GffCompare Filter FASTA Column arrange XPath Sub-sample sequences files Filter sequences by ID find in reference Filter Sort Select Select Extract features Filter GFF data by attribute Filter GFF data by feature count Filter GTF data by attribute values_list

Join, Subtract and Group

Column join Transpose Reverse Datamash Datamash Subtract Join two Datasets Compare two Datasets Group

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Genomic File Manipulation

Convert Formats

Convert Tabular-to-FASTA FASTA-to-Tabular Tabular to FASTQ GFA to FASTA Thermo msconvert Extract MAF blocks CrossMap Wig CrossMap VCF CrossMap GFF CrossMap BED Stitch Gene blocks CrossMap BAM mz to sqlite idpQuery bed to protein map Convert gffCompare annotated GTF to BED Map peptides to a bed file Resize coordinate window gffread msms_extractor bax2bam Image Montage Image Converter Create InterMine Interchange idconvert msconvert Subset Peak List idconvert Convert GTF to BED12 twoBitToFa Convert BAM to ScIdx bigWigToBedGraph Convert BAM CrossMap region samtools BAM to CRAM ab1 to FASTQ converter Compress file(s) xmlstarlet AXT to concatenated FASTA AXT to FASTA AXT to LAV BED-to-GFF GFF-to-BED LAV to BED MAF to BED MAF to Interval MAF to FASTA Wiggle-to-Interval SFF converter GTF-to-BEDGraph Wig/BedGraph-to-bigWig BED-to-bigBed Convert genome coordinates

FASTA/FASTQ

Select high quality segments Build base quality distribution Compute sequence length Concatenate FASTQ Trimmer FASTQ Quality Trimmer FASTQ to FASTA FASTQ Summary Statistics FASTQ to Tabular Combine FASTA and QUAL Filter FASTQ FASTQ Groomer Manipulate FASTQ FASTQ Masker FASTQ de-interlacer FASTQ interlacer FASTQ joiner FASTQ splitter Rename sequences Reverse-Complement Trim sequences FASTQ to FASTA Compute quality statistics Draw quality score boxplot Quality format converter Filter by quality FASTA Width RNA/DNA Trimmomatic Collapse FASTQE fastp Filter sequences by length FASTA-to-Tabular Tabular to FASTQ Tabular-to-FASTA Fasta regular expression finder BBTools: BBduk Remove sequencing artifacts Exonerate FastQC Trim Galore! UMI-tools count UMI-tools extract Sickle seqtk_sample UMI-tools group UMI-tools whitelist FLASH seqtk_comp seqtk_mutfa seqtk_hety seqtk_cutN seqtk_mergefa seqtk_trimfq seqtk_fqchk seqtk_randbase seqtk_subseq seqtk_dropse seqtk_mergepe seqtk_seq seqtk_listhet mQC Fasta Statistics filtlong Clip Cutadapt Draw nucleotides distribution chart Barcode Splitter Get crosslinked nucleotides faSplit Trim putative adapter sequence Create binary barcodes Extract barcodes Extract alignment ends Merge PCR duplicates Remove spurious Remove 3’-end nts Je-Clip Je-Demultiplex Je-MarkDuplicates Je-Demultiplex-Illu UMI-tools deduplicate FASTA Merge Files and Filter Unique Sequences Thread nucleotides onto a protein alignment (back-translation) Filter sequences by mapping lighter fastq-join Split Fasta gfastats RNA-seq Rcorrector Pear Calculate sequence complexity SeqKit statistics SeqKit fx2tab AdapterRemoval: remove adapter sequences SeqKit locate SeqKit locate Convert Compute quality statistics Draw quality score boxplot

Quality Control

MultiQC QualiMap Counts QC FASTQ info

SAM/BAM

Split Filter BAM Pileup-to-Interval Filter pileup Convert SAM Merge BAM Files Generate pileup Samtools flagstat Samtools mpileup RmDup Slice Samtools view Samtools reheader QualiMap BamQC QualiMap Multi-Sample BamQC Operate on and transform BAM Tag pileup frequency Samtools markdup Samtools merge Samtools fastx Samtools fixmate Samtools stats Samtools idxstats Filter SAM or BAM, output SAM or BAM Samtools split Samtools bedcov Samtools depth Samtools sort Samtools coverage BAM filter Split BAM by reads mapping status Split BAM into paired- and single-end Split BAM by reference Split BAM by read tag value Samtools calmd Samtools phase BamHash BamHash BamUtil diff Samtools ampliconclip revertR2orientationInBam

BED

bedtools ExpandBed bedtools NucBed bedtools GroupByBed bedtools Intersect intervals bedtools OverlapBed bedtools getfasta bedtools MaskFastaBed bedtools MergeBED bedtools Multiple Intersect bedtools SortBED bedtools BAM to BED bedtools ComplementBed bedtools WindowBed bedtools AnnotateBed bedtools JaccardBed bedtools TagBed bedtools ClosestBed bedtools SpacingBed bedtools Merge BedGraph files bedtools MakeWindowsBed bedtools Compute both the depth and breadth of coverage bedtools Genome Coverage bedtools MultiCovBed bedtools SubtractBed bedtools ClusterBed bedtools SlopBed bedtools FlankBed bedtools LinksBed bedtools BED12 to BED6 bedtools BED to BAM bedtools MapBed bedtools BED to IGV bedtools ShuffleBed bedtools ReldistBed bedtools RandomBed bedtools BEDPE to BAM bedtools FisherBed GffCompare bedtools Convert from BAM to FastQ Create a BedGraph of genome coverage Merge BedGraph files Create a histogram of genome coverage

VCF/BCF

VCFfilter: VCFcheck: VCFaddinfo: VCFtoTab-delimited: VCFleftAlign: VCFcombine: VCFsort: VCFhetHomAlleles: VCFrandomSample: VCF-BEDintersect: VCFgenotypes: VCFfixup: VCFgenotype-to-haplotype: VcfAllelicPrimitives: VCFbreakCreateMulti: VCF-VCFintersect: vcfanno VCFannotate: VCFcommonSamples: VCFflatten: VCFannotateGenotypes: VCFselectsamples: ococo Variant Annotator VCFdistance: VCFdistance: Intersect Merge Merge Compare Annotate Slice VCF Subset

Nanopore

NanoPlot medaka variant tool FLAIR correct FLAIR collapse CoNvex medaka variant pipeline medaka consensus pipeline medaka consensus tool NanoComporeDB ont_fast5_api: Multi to single ont_fast5_api: Single to multi ont_fast5_api: Compress ont_fast5_api: Subset Nanopolish polyA Nanopolish eventalign Nanopolish methylation Nanopolish variants SampComp NanopolishComp: FreqMethCalculate NanopolishComp: EventalignCollapse Porechop Extract time Show nucleotide Show quality Extract reads Extract FASTQ Read length statistics Plot signals Plot performance Generate histogram Collector’s curve Generate box-whisker Get longest read Extract nanopore events Pycoqc Clair3

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Common Genomics Tools

Operate on Genomic Intervals

Complement Cluster Base Coverage Profile Annotations Table to GFF3 Translate BED transcripts Concatenate Join Translate BED Sequences Filter BED on splice junctions Aggregate datapoints

Fetch Sequences / Alignments

Extract Genomic DNA Gene length and GC content FragGeneScan SeqKit locate Gene BED To Exon/Intron/Codon BED Extract Pairwise MAF blocks Extract MAF blocks Split MAF blocks Stitch MAF blocks Stitch Gene blocks MAF Coverage Stats Join MAF blocks Filter MAF blocks Filter MAF blocks Extract MAF by block number Reverse Complement Filter MAF

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Genomics Analysis

Annotation

seq2HLA MITOS Busco TB-Profiler Profile Integron Finder Funannotate predict annotation Funannotate compare annotateMyIDs GffCompare CPAT goseq OptiType Prokka Roary nhmmer hmmbuild hmmscan phmmer jackhmmer nhmmscan hmmsearch KofamScan Table to GFF3 MOB-Recon MOB-Typer ectyper sistr_cmd Antismash ChIPseeker progressiveMauve Convert XMFA to gapped GFF3 MLST List MLST Genbank to GFF3 MITOS2 Exonerate FastANI TRANSIT Tn5Gaps TRANSIT Resampling TRANSIT HMM TRANSIT Gumbel TETyper Train Augustus Augustus fargene KOBAS Annotate KOBAS Identify Convert GFF3 gProfiler SNPense gProfiler Random gProfiler GOSt gProfiler Orth gProfiler Convert ABRicate ABRicate List BlastXML to gapped GFF3 Maker Compute socru Train SNAP Map annotation ids fgsea Filter with SortMeRNA Spaln: align cDNA or Protein to genome GOSlimmer GOEnrichment Genome annotation statistics Hammock - cluster peptides Bakta psortb SignalP 3.0 Promoter 2.0 TMHMM 2.0 RXLR Motifs Funannotate functional Funannotate assembly clean Sort assembly bacteriophage annotation PfamScan GECCO WoLF PSORT Metagenome Contributions Format Compare BIOM tables Predict Metagenome Categorize tRNA prediction tRNA and tmRNA TransTermHP estimate-energy fix-fasta-headers filter-annotated-entries add-read-counts find-boxes filter-by-energy extract-boxed-sequences segmentation-fold Gubbins ProbMetab Tool LC/MS matching Nucleosome Predictions OrthoFinder miRanda DotKnot Blast2GO alimask hmmalign hmmconvert hmmemit hmmfetch Nucleotide subsequence search GotohScan CryptoGenotyper Annotate with DGI Annotate with DGI HHsearch ABRicate Summary Glimmer ICM builder Glimmer3 Glimmer3 TB Variant Report TB Variant Filter lorikeet spoligotyping SpoTyping RepeatModeler RepeatMasker scanMotifGenomeWide annotatePeaks findMotifsGenome Converts GTF to Annotations file for Homer SnpSift GeneSets hamronize hamronize: summarize List spaln parameter tables InterProScan legsta TEfinder ISEScan Miniprot align netboxr PlasmidFinder Miniprot index Red edta

Multiple Alignments

ClustalW SINA Gecko Chromeister MAF Coverage Stats Mummer Mummerplot Delta-Filter Nucmer DNAdiff Show-Coords Kc-Align Automated multiple sequence Select Sequences MSABOOT Hammock - cluster peptides Format cd-hit outputs MUSCLE Compalignp MAFFT MAFFT add cd-hit

Assembly

BlobToolKit YAHS Quast Hifiasm_meta Get annotated regions from genbank files (getorganelle) Get organelle from reads Cactus: export NextDenovo Hifiasm Bionano Hybrid Scaffold Trycycler cluster Trycycler consensus Trycycler partition Trycycler reconcile/msa Trycycler subsample Canu assembler MITObim TrimN Purge overlaps AEGeAn ParsEval AEGeAn LocusPocus AEGeAn GAEVAL AEGeAn CanonGFF3 SALSA Shasta Lordec NOVOplasty MEGAHIT IDBA-TRAN Shovill Racon Minia Flye miniasm ABySS Create assemblies with Unicycler IDBA-UD IDBA-HYBRID SPAdes VelvetOptimiser pilon WTDBG metaSPAdes DISCO rnaSPAdes Meryl Assemble with MIRA v3.4 Edena (assembling) Edena (overlapping) SOPRA with prebuilt contigs SSAKE CRISPR Recognition Tool detect CRISPR sequences Merqury GenomeScope PretextMap Filter and merge MitoHiFi Raven RagTag TGS-GapCloser HyPo rnaviralSPAdes Cactus plasmidSPAdes metaviralSPAdes metaplasmidSPAdes coronaSPAdes biosyntheticSPAdes LINKS gfastats velvetg velveth cap3 Smudgeplot Hapo-G minipolish instaGRAAL necat BiSCoT velvetg velveth

Mapping

RNA STARSolo BBTools: BBMap RNA STAR Parse blast XML output Map with BWA Megablast Lastz paired reads LASTZ Map with Bowtie for Illumina Map with minimap2 HISAT2 Bismark Mapper Map with KMA STAR-Fusion Bismark Deduplicate Bismark Pretty Report Bismark Meth. Extractor Bowtie2 segemehl Owler Mapper Bismark Map with BWA-MEM LASTZ_D TopHat Map with Bowtie for SOLiD Winnowmap Align sequences BWA-MEM2 Map with BFAST Map with PerM Re-align with SRMA Map with Mosaik

Variant Calling

faToVcf bcftools stats bcftools roh bcftools reheader bcftools query bcftools setGT bcftools frameshifts bcftools filter bcftools csq bcftools convert to vcf bcftools convert from vcf bcftools annotate bcftools call bcftools consensus VarScan somatic Naive Variant Caller (NVC) VarScan VarScan copynumber Strelka Germline sansa annotate Strelka Somatic VarScan mpileup Delly filter Delly merge Delly call Delly long-read (lr) Delly classify Delly cnv vcfanno JasmineSV Iris Variant Frequency Plot DCS mutations to tags/reads: SnpSift Filter DCS mutations to SSCS stats: Call specific mutations in reads: LUMPY LUMPY preprocessing Lofreq filter Call variants plink ARTIC minion cuteSV sniffles VarDict Control-FREEC GATK4 Mutect2 bcftools concat SnpEff eff: Realign reads Add LoFreq alignment quality scores Insert indel qualities seqwish odgi viz odgi build vg view vg deconstruct vg convert snippy-core snippy-clean_full_aln snippy bcftools merge VCFselectsamples: VCFannotateGenotypes: VCFdistance: VCFflatten: VCFcommonSamples: VCFannotate: VCF-VCFintersect: VCFbreakCreateMulti: VcfAllelicPrimitives: VCFgenotype-to-haplotype: VCFfilter: VCFfixup: VCFgenotypes: VCF-BEDintersect: VCFrandomSample: VCFhetHomAlleles: VCFsort: VCFprimers: VCFcombine: VCFleftAlign: VCFtoTab-delimited: VCFaddinfo: VCFcheck: bcftools norm bcftools color-chrs bcftools cnv SNP distance matrix Tag pileup frequency Finds SNP sites ExomeDepth FreeBayes SnpEff build: basil bcftools gtcheck bcftools isec bcftools mpileup bcftools split-vep bcftools view BBTools: call variants Beagle SnpSift Intervals SnpSift rmInfo SnpSift Variant Type SnpSift Annotate SnpSift CaseControl SnpEff chromosome-info: SnpSift Extract Fields SnpSift vcfCheck bcftoolsView BamLeftAlign VT normalize SnpEff databases: SnpSift GeneSets SnpSift dbNSFP SnpSift dbNSFP SnpEff download: SnpEff eff: SnpEff Ensembl CDS SnpEff to Peptide fasta Variant Annotator SnpSift Intervals SnpSift Annotate SnpSift Filter SnpSift CaseControl Get homopolymer run length DeepVariant KING ARTIC guppyplex pharmCAT Predict variant effects breseq Convert VCF to MAF

Genome editing

CRISPR Studio MAGeCKs test MAGeCK mle MAGeCK GSEA MAGeCK count MAGeCK pathway parse mykrobe predict AmpliCan

RNA-Seq

IsoformSwitchAnalyzeR blockbuster

RNA Analysis

RPKM Count RPKM Saturation BAM to Wiggle BAM/SAM Mapping Stats Clipping Profile Gene Body Coverage (BAM) Gene Body Coverage (Bigwig) Infer Experiment Inner Distance Junction Annotation Junction Saturation Read GC Read NVC Read Distribution Read Duplication Read Quality featureCounts Train a CheRRI model using RRIs Filter Combined Transcripts eXpress Cuffmerge Cufflinks Cuffdiff Cuffcompare rnaQUAST Remove Unwanted Variation FEELnc MiGMAP scPipe Seurat TEtranscripts TransDecoder ChiRA collapse ChiRA merge ChiRA map ChiRA qauntify ChiRA extract Trinotate footprint Cuffnorm cummeRbund htseq-count Salmon quant DESeq2 StringTie StringTie merge Align reads and estimate abundance Trinity sRNAPipe GraphProt Visualize Slamdunk Alleyoop QualiMap Counts QC QualiMap RNA-Seq QC tximport maSigPro Generate SuperTranscripts Build expression matrix Compute contig Ex90N50 statistic and Ex90 transcript count Filter low expression transcripts Differential expression analysis Filter with SortMeRNA Salmon quantmerge GLASSgo IntaRNA Kallisto pseudo Kallisto quant edgeR Cross-contamination Barcode Filter Evaluation of RRIs using CheRRI FPKM Count RNA fragment size Deletion Profile Insertion Profile Mismatch Profile Hexamer frequency Transcript Integrity Number limma DEXSeq DEXSeq-Count plotDEXSeq Extract and cluster differentially expressed transcripts EGSEA Select Sequences Cofold RNAz Cluster Dr. Disco (classify) Dr. Disco (fix) Dr. Disco (bam-extract) Dr. Disco (integrate) Dr. Disco (detect) MEA CMCV RNAz Randomize Aln RNAz Select Seqs RNAz windows Annotate RNAz Annotate DESeq2/DEXSeq output tables LocARNA Multiple Aligner cmv ribotaper part 2: metagene analysis for P-sites definition ribotaper part 3: ribosome profiling ribotaper part 1: creation of annotation files PIPmiR PIPELINE NASTIseq FlaiMapper TargetFinder Get motifs from AREsite2 FuMa RNAlien BlockClust Generate gene to transcript map RNASeq samples quality check Describe samples Partition genes into expression clusters Fit a BUM model Identify optimal scoring subnetwork Calculate a Heinz score ssHMM pizzly RCAS RNAcode RNAz RNAshapes RNAfold IDR RNAcofold RNAalifold segemehl Sailfish Cuffquant RNAeval RNAplex RNA2Dfold RNApaln RNAplot RNAsnoop Kinfold RNAaliduplex RNAduplex RNAdistance RNApdist RNALfold RNAPKplex RNAup RNALalifold RNAinverse RNAheat RNAsubopt cmalign cmsearch cmscan cmpress cmbuild cmstat remuRNA RNAsnp LocARNA PARalyzer CIRCexplorer RNAcommender Tophat Fusion Post blockbuster Kinwalker antaRNA RNABOB Get RT Stop Counts RNA Structure Prediction Iterative Mapping Reactivity Calculation Extract CuffDiff MiRDeep2 Mapper MiRDeep2 Quantifier MiRDeep2 RSEM prepare reference RSEM calculate expression RSEM trinity fasta to gene map GenomicSuperSignature barrnap Arriba Draw Fusions Arriba Get Filters Arriba CIRCexplorer2 riboWaltz riboWaltz-plot CEMiTool miRNAture

Peak Calling

PEAKachu MACS SICER CCAT Genrich DiffBind MACS2 bdgcmp MACS2 bdgbroadcall MACS2 refinepeak MACS2 bdgdiff MACS2 bdgpeakcall MACS2 predictd MACS2 randsample MACS2 filterdup MACS2 callpeak zerone PureCLIP JAMM Piranha htseq-clip DEWSeq DEWSeq CLIP Peakcaller

Epigenetics

Hicup to juicer converter Hicup Digester Hicup Pipeline Hicup Truncater cooler csort with tabix Filter SEACR MOABS Minfi Preprocess Quantile Minfi Rset Minfi Drop SNPs Minfi Mset Minfi Read 450k Minfi Preprocess Funnorm cooler_makebins Minfi DMP cooler_cload_tabix Hicup Filter Hicup Deduplicator Hicup Mapper cooler_balance Minfi DMR Minfi Get CN Minfi Get Beta Minfi Get SNPs Minfi Map to Genome Minfi Get M Minfi QC Infinium Human Methylation BeadChip metilene bwameth MethylDackel EpiCSeg - Chromatin segmentation

Phylogenetics

PICRUSt2 Generation of shuffled predictions PICRUSt2 Pathway abundance inference PICRUSt2 Hidden state prediction (HSP) PICRUSt2 Add descriptions HyPhy-Summary HyPhy-RELAX HyPhy-FUBAR HyPhy-FEL HyPhy-BUSTED Annotate Pangolin HyPhy-PRIME HyPhy-BGM HyPhy-GARD HyPhy-aBSREL HyPhy-FADE HyPhy-SM2019 HyPhy-MEME HyPhy-SLAC T-Coffee sarscov2formatter Phyogenetic reconstruction with RAxML GeneSeqToFamily preparation PhyML sarscov2summary Replace ambiguous codons HyPhy-CFEL HyPhy-Conv PICRUSt2 Metagenome prediction PICRUSt2 Full pipeline PICRUSt2 Sequence placement Gene Copy Number Finder hcluster_sg parser ETE lineage generator ETE species tree generator ETE GeneTree splitter Homology Classifier and Filter ETE taxa DB generator ETE mod TreeBeST best Species tree generator Gene Align and Family Aggregator TreeBeST best FASTA header converter hcluster_sg BLAST parser NextAlign Nextclade UShER matUtils UShER SNP distance matrix

Phenotype Association

VCF to pgSnp snpFreq FunDO HVIS Separate pgSnp alleles CTD aaChanges phyloP SIFT g:Profiler DAVID LD PASS GPASS BEAM LPS MasterVar to pgSnp

Single-cell

CITE-seq-Count Import Anndata and loom Export AnnData and loom files Manipulate AnnData Inspect AnnData Manipulate loom object DropletUtils DropletUtils Read10x DropletUtils emptyDrops Alevin Filter Inspect and manipulate Normalize Plot Remove confounders Slice Image Cluster, infer trajectories and embed Scanpy ParameterIterator Scater: t-SNE plot Scater: PCA plot Scater: plot expression frequency Scater: plot library QC Scater: normalize SCE Scater: filter SCE Scater: calculate QC metrics Cluster Inspection using RaceID Initial processing using RaceID Clustering using RaceID Lineage computation using StemID Lineage Branch Analysis using StemID MuSiC Deconvolution Construct Expression Set Object Inspect Expression Set Object MuSiC Compare Manipulate Expression Set Object scran_normalize

Spatial Omics

BaSiC Illumination ASHLAR UNetCoreograph UnMicst s3segmenter MCQUANT

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Genomics Toolkits

Picard

MarkDuplicatesWithMateCigar ReorderSam MarkDuplicates SortSam AddOrReplaceReadGroups QualityScoreDistribution CleanSam MeanQualityByCycle CollectBaseDistributionByCycle NormalizeFasta EstimateLibraryComplexity Collect Alignment Summary Metrics CollectWgsMetrics FastqToSam MergeBamAlignment FilterSamReads CollectRnaSeqMetrics RevertOriginalBaseQualitiesAndAddMateCigar ValidateSamFile CollectGcBiasMetrics Downsample SAM/BAM SamToFastq RevertSam BedToIntervalList MergeSamFiles FixMateInformation AddCommentsToBam CollectInsertSizeMetrics ReplaceSamHeader SAM/BAM Alignment Summary Metrics BAM Index Statistics Add or Replace Groups Estimate Library Complexity Insertion size metrics Paired Read Mate Fixer CollectHsMetrics Picard Collect Sequencing Artifact Metrics

deepTools

bamCompare bamCoverage bamPEFragmentSize bigwigCompare plotHeatmap correctGCBias multiBamSummary plotPCA computeMatrix computeGCBias multiBigwigSummary plotProfile plotCorrelation plotCoverage plotFingerprint computeMatrixOperations alignmentsieve plotEnrichment estimateReadFiltering Hicup Deduplicator

Gemini

GEMINI query GEMINI database info GEMINI load GEMINI pathways GEMINI windower GEMINI annotate GEMINI amend GEMINI gene_wise GEMINI burden GEMINI stats GEMINI actionable_mutations GEMINI lof_sieve GEMINI fusions GEMINI roh GEMINI set_somatic GEMINI qc GEMINI interactions GEMINI inheritance pattern

EMBOSS

pepwindow pepwindowall degapseq infoseq needle patmatdb marscan oddcomp fuzztran helixturnhelix merger newcpgseek extractseq maskfeat codcmp supermatcher equicktandem cutseq tranalign cai custom newcpgreport noreturn sigcleave union preg msbar getorf pepstats digest extractfeat revseq skipseq splitter iep transeq tcode octanol banana maskseq geecee pepwheel cpgplot notseq water seqret pepinfo megamerger trimseq showfeat palindrome pasteseq lindna plotorf etandem cai dreg syco compseq sixpack btwisted prettyseq diffseq newseq chaos plotcon dottup pepnet textsearch chips prettyplot fuzzpro primersearch wobble vectorstrip seqmatchall wordcount shuffleseq garnier trimest cusp dotpath matcher descseq hmoment einverted cirdna tmap nthseq checktrans cpgreport polydot dan sirna pepcoil isochore est2genome epestfind coderet fuzznuc charge freak biosed twofeat wordmatch backtranseq antigenic dotmatcher

NCBI Blast

Krona pie chart BLAST XML to tabular NCBI BLAST+ database info NCBI BLAST+ blastdbcmd entry(s) NCBI BLAST+ blastn NCBI BLAST+ blastp NCBI BLAST+ blastx NCBI BLAST+ convert2blastmask NCBI BLAST+ dustmasker NCBI BLAST+ makeblastdb NCBI BLAST+ makeprofiledb NCBI BLAST+ rpsblast NCBI BLAST+ rpstblastn NCBI BLAST+ segmasker NCBI BLAST+ tblastn NCBI BLAST+ tblastx Diamond view Diamond Diamond makedb Kraken-translate Kraken-filter BLAST Reciprocal Best Hits (RBH) Sub-sample sequences files BLAST top hit descriptions BBTools: call variants BBTools: BBduk Kraken taxonomic report NCBI get species taxids Magic-BLAST: map large RNA or DNA sequences

HiCExplorer

hicTransform hicMergeLoops hicCorrelate hicCompartmentalization chicSignificantInteractions scHicQualityControl chicPlotViewpoint chicDifferentialTest chicAggregateStatistic chicViewpoint hicPlotViewpoint hicPlotSVL hicPlotMatrix hicPlotDistVsCounts hicPlotAverageRegions hicPCA hicFindTADs hicValidateLocations hicDetectLoops hicCompareMatrices hicAverageRegions hicAggregateContacts hicCorrectMatrix hicNormalize hicSumMatrices hicMergeMatrixBins hicConvertFormat hicAdjustMatrix hicBuildMatrix hicFindRestSite hicInfo hicQuickQC chicViewpointBackgroundModel chicQualityControl hicDifferentialTAD hicHyperoptDetectLoops hicMergeDomains scHicCorrectMatrices scHicPlotConsensusMatrices scHicPlotClusterProfiles scHicNormalize scHicCreateBulkMatrix scHicMergeToSCool scHicMergeMatrixBins scHicInfo scHicDemultiplex scHicConsensusMatrices scHicClusterSVL scHicClusterMinHash scHicClusterCompartments scHicCluster scHicAdjustMatrix hicPlotTADs

RAD-seq

BayeScan Stacks: assemble read pairs by locus Stacks: cstacks Stacks2: process shortreads Stacks2: kmer filter Stacks2: clone filter Stacks2: tsv2bam Stacks2: reference map Stacks2: de novo map Stacks2: process radtags Stacks2: populations Stacks2: gstacks Stacks2: sstacks Stacks2: cstacks Stacks2: ustacks Stacks: populations Stacks: clone filter Stacks: statistics Stacks: sstacks Stacks: genotypes Stacks: de novo map Stacks: ustacks Stacks: process radtags Stacks: reference map Stacks: rxstacks Stacks: pstacks

GraphClust

Image Converter NSPDK_candidateClusters Structure to GSPAN Preprocessing pgma_graphclust NSPDK_sparseVect locarna_graphclust fasta_to_gspan cluster_collection_report cmfinder Align GraphClust cluster Aggregate and filter alignment metrics Graphclust glob_report collect clusters Motif_Finder_Plot Build covariance models Search covariance model(s) Summary statistics

MiModD

MiModD Read Alignment MiModD File Information MiModD Report Variants MiModD Extract Variant Sites MiModD NacreousMap MiModD VCF Filter MiModD Coverage Statistics MiModD Convert MiModD Variant Calling MiModD Run Annotation MiModD Reheader MiModD Rebase Sites MiModD Deletion Calling (for PE data) MiModD Sort

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Metagenomics

Metagenomic Analysis

CAT summarise CAT bins CAT add_names Krakentools: Combine multiple Kraken reports Kleborate Unpack pathway abundances Make strain profiles Normalize Renormalize Rename features Reduce Join (merge) HUMAnN Krakentools: Calculates alpha diversity Kraken2 dada2: makeSequenceTable dada2: plotQualityProfile dada2: mergePairs dada2: assignTaxonomy and addSpecies dada2: sequence counts dada2: plotComplexity dada2: learnErrors dada2: dada dada2: removeBimeraDenovo dada2: filterAndTrim MetaEuk Easy Predict staramr LAST-train MT2MQ Join VSearch search HUMAnN2 Associate Barplot Create a genus level gene families file Reduce Regroup Rename Renormalize Normalize Split stratified table Split Make strain profiles Unpack pathway abundances to show genes included LASTal dRep dereplicate dRep compare LASTdb LAST-split MAF-convert mash screen MetaGeneAnnotator mash sketch sixgill merge sixgill filter sixgill build sixgill makefasta CAT contigs khmer: Filter reads khmer: Filter reads khmer: Extract partitions khmer: Abundance Distribution khmer: Count Median khmer: Sequence partition all-in-one khmer: Normalize By Median khmer: Abundance Distribution (all-in-one) Kraken Kraken-report Krona pie chart Kraken-filter Kraken-translate CAT prepare MaxBin2 Group abundances PlasFlow Kraken-mpa-report Vegan Diversity Vegan Fisher Alpha Vegan Rarefaction VSearch sorting VSearch chimera detection VSearch clustering VSearch masking VSearch alignment VSearch dereplication VSearch shuffling Krakentools: Convert kraken report file Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) CoverM contig CoverM genome Perform metadata association Barplot Regroup Split a HUMAnN table Split Customize the marker sequences and metadata Extract the marker sequences and metadata Merge Krakentools: Extract Kraken Reads By ID Krakentools: Convert kraken report file MetaPhlAn Compare outputs of HUMAnN2 for several samples Combine MetaPhlAn2 and HUMAnN2 outputs Format MetaPhlAn2 VALET GDCWebApp Salmonella Subtyping Nonpareil MetaPhlAn2 Format MetaPhlAn2 Generate heatmap metagenomeSeq Normalization Kraken taxonomic report Convert Kraken Scoary jellyfish LotuS2 InStrain Profile InStrain Compare Estimate Abundance at Taxonomic Level MaAsLin 2 MALT analyzer MEGAN: Generate a MEGAN rma6 file MEGAN: Generate RMA files MEGAN Blast2LCA: apply LCA alignment Calculate contig depths MetaBAT2 Binning refiner Create phyloseq object Phyloseq: plot ordination Phyloseq: plot alpha diverstiy measure CONCOCT CONCOCT: Generate the input coverage table CONCOCT: Cut up contigs CONCOCT: Extract a fasta file CONCOCT: Merge cut clusters MEGAN: Get information MEGAN: Generate a MEGAN rma6 file MEGAN: meganize a DIAMOND file MEGAN: Extract reads ITSx DAS Tool Converts genome bins in fasta format Recentrifuge ALDEx2 ANCOM-BC CheckM taxonomy_wf CheckM tree CheckM lineage_wf CheckM tree_qa CheckM analyze CheckM tetra CheckM qa CheckM taxon_set CheckM plot CheckM lineage_set SRST2 Kraken-biom VAPOR Polypolish SemiBin: Contig annotations SemiBin SemiBin: Train SemiBin: Generate sequence features SemiBin: Group the contigs SemiBin: Concatenate fasta files Format cd-hit outputs ampvis2 alpha diversity ampvis2 boxplot ampvis2 core community analysis ampvis2 export fasta ampvis2 frequency plot ampvis2 heatmap ampvis2 load ampvis2 merge ampvis2 data sets ampvis2 merge replicates ampvis2 octave plot ampvis2 ordination plot ampvis2 OTU network plot ampvis2 rank abundance plot ampvis2 rarefaction curve ampvis2 set metadata ampvis2 subset samples ampvis2 subset data ampvis2 timeseries plot ampvis2 venn diagram DRAM strain annotations DRAM distill DRAM annotate DRAM merge multiple annotations DRAM find neighborhoods

Qiime

Collapse samples Make OTU table Perform open-reference OTU picking Closed-reference OTU picking Count the sequences Format Fastq sequences and barcode data Count sequences Create three-dimensional PCoA plots Plot heatmap of OTU table Pick representative set of sequences Run join_paired_ends on multiple files Align sequences Perform alpha rarefaction Perform open-reference OTU picking Perform closed-reference OTU picking Run a core set of QIIME diversity analyses Calculate alpha diversity Split fastq libraries Filter OTUs from an OTU table Perform jackknifed UPGMA clustering Filter taxa from an OTU table Perform OTU picking Analyze statistical significance of sample groupings Make taxonomy summary charts Build a UPGMA tree Filter fasta Filter sequence alignment Assign taxonomy Make phylogeny Summarize taxa Calculate beta diversity Split libraries Filters samples from an OTU table Perform taxonomy summaries and plots Run split_libraries_fastq on multiple files Compute beta diversity distance matrices and generate PCoA plots Check user’s metadata mapping file

Mothur

Screen.seqs Make.contigs Get.label Chimera.vsearch Chimera.pintail Split.abund Mimarks.attributes Summary.single Chop.seqs Remove.otulabels Get.sabund Make.sra Make.group Trim.seqs Nmds List.otulabels Create.database Deunique.tree Biom.info Pairwise.seqs Merge.count Pcr.seqs Taxonomy-to-Krona Split.groups Classify.tree Make.fastq Pcoa Summary.shared Sort.seqs Remove.dists Make.lefse Cluster.classic Filter.seqs Unique.seqs Rename.seqs Cooccurrence Parse.list Get.group Make Design Get.dists Get.otulist Merge.groups Otu.association Merge.files Filter.shared Phylo.diversity Sffinfo Sub.sample Deunique.seqs Chimera.perseus Amova Align.check Align.seqs Classify.rf Dist.seqs Pre.cluster Libshuff Metastats Get.rabund Get.otus Otu.hierarchy Trim.flows Cluster.fragments Rarefaction.shared Classify.seqs Phylotype unifrac.unweighted Tree.shared Get.otulabels Count.seqs Consensus.seqs Collect.shared Corr.axes Summary.seqs Anosim Remove.seqs Get.communitytype Cluster.split Summary.tax Fastq.info unifrac.weighted Get.seqs Bin.seqs Degap.seqs Chimera.ccode Primer.design Seq.error Remove.groups Mantel Lefse Heatmap.bin Clearcut Get.sharedseqs Chimera.bellerophon Cluster Sens.spec Make.shared Chimera.slayer Remove.lineage Reverse.seqs Dist.shared Shhh.flows Get.lineage Merge.taxsummary Hcluster Make.lookup Remove.rare Collect.single Rarefaction.single Get.groups Chimera.check Heatmap.sim Get.relabund Make.biom Classify.otu Merge.sfffiles Summary.qual Venn List.seqs Homova Pca Remove.otus Parsimony Shhh.seqs Get.oturep Count.groups Get.mimarkspackage Normalize.shared Indicator Get.coremicrobiome Chimera.uchime

DNA Metabarcoding

obitab obistat obisort obiconvert obiclean obiuniq obigrep obiannotate NGSfilter Illuminapairedend

Virology

ivar filtervariants ivar trim ivar variants ivar removereads ivar consensus ivar getmasked Read It and Keep snipit Freyja: Call variants Freyja: Demix Freyja: Bootstrapping Freyja: Aggregate and visualize Cojac: mutbamscan Cojac: pubmut Cojac: tabmut

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Proteomics, Metabolomics, Chemistry

Proteomics

MALDIquant preprocessing MALDIquant peak detection MaxQuant Phosphopeptide ANOVA MaxQuant Phosphopeptide Preprocessing MSstats MaxQuant MaxQuant (using mqpar.xml) MSstatsTMT ConsensusID metaQuantome: visualize metaQuantome: stat metaQuantome: filter metaQuantome: expand metaQuantome: database eggNOG Mapper MSI combine PSMFeatureExtractor MetaProteomeAnalyzer metaQuantome: create samples file pyteomics DIAlignR FASTG2Protlib-Peptides FASTG2Protlib-Validate NovorAdapter LuciphorAdapter AssayGeneratorMetabo SiriusAdapter MSFraggerAdapter MSGFPlusAdapter MSI plot spectra MSI mz images MSI preprocessing PeakPickerHiRes RNAMassCalculator QualityControl RNPxlXICFilter OpenSwathConfidenceScoring MultiplexResolver PSM-Fragment Validator Remove protonation state idpQuery OpenSwathFeatureXMLToTSV OpenSwathDIAPreScoring MapStatistics DigestorMotif FeatureLinkerLabeled XTandemAdapter SpectraFilterWindowMower OpenSwathWorkflow QCMerger IDMapper IDMassAccuracy IDRTCalibration IDSplitter MRMTransitionGroupPicker MapAlignerIdentification IsobaricAnalyzer ERPairFinder ClusterMassTraces ClusterMassTracesByPrecursor CometAdapter CompNovo CompNovoCID IDMerger MetaboliteSpectralMatcher RTEvaluation QCExporter SpectraFilterNormalizer InternalCalibration MassTraceExtractor Digestor PepNovoAdapter PeptideIndexer MapRTTransformer DTAExtractor OpenSwathAssayGenerator MetaProSIP SequenceCoverageCalculator ProteinQuantifier IDConflictResolver PeakPickerWavelet FuzzyDiff PeakPickerIterative Decharger MzMLSplitter FileConverter SpectraFilterNLargest MassCalculator SpectraFilterThresholdMower MapAlignerPoseClustering QCEmbedder Epifany SpectraMerger PTModel OpenSwathDecoyGenerator ProteinInference TargetedFileConverter TextExporter TOFCalibration TransformationEvaluation IDRipper XMLValidator SvmTheoreticalSpectrumGeneratorTrainer MascotAdapterOnline SpectraSTSearchAdapter SpectraFilterSqrtMower SpectraFilterMarkerMower SemanticValidator SpecLibSearcher LabeledEval MapAlignerSpectrum SpecLibCreator MaRaClusterAdapter SimpleSearchEngine PrecursorIonSelector SeedListGenerator RTModel FeatureFinderCentroided RNPxlSearch SpectraFilterParentPeakMower TICCalculator IDFilter NucleicAcidSearchEngine MRMMapper OMSSAAdapter EICExtractor MyriMatchAdapter SpectraFilterBernNorm MSSimulator BaselineFilter RNADigestor CVInspector MSI Qualitycontrol DecoyDatabase ExternalCalibration FalseDiscoveryRate FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMRM FeatureFinderMultiplex FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FFEval FidoAdapter FileFilter FileInfo FileMerger GNPSExport AccurateMassSearch DatabaseFilter DeMeanderize FeatureFinderSuperHirn MSI classification OpenSwathMzMLFileCacher OpenSwathRewriteToFeatureXML IDPosteriorErrorProbability IDFileConverter MSI data exporter MSI segmentation MSI filtering IDScoreSwitcher OpenPepXL XFDR MapAlignerTreeGuided PercolatorAdapter MapNormalizer MascotAdapter MetaboliteAdductDecharger MRMPairFinder MSstatsConverter MzTabExporter NoiseFilterGaussian EncyclopeDIA NoiseFilterSGolay ConvertFastaToPrositCSV EncyclopeDIA Quantify OpenPepXLLF Walnut ConvertPrositCSVToLibrary OpenSwathChromatogramExtractor OpenSwathAnalyzer SearchToLib OpenSwathFileSplitter ConvertLibraryToBlib OpenSwathRTNormalizer PhosphoScoring HighResPrecursorMassCorrector PrecursorMassCorrector QCCalculator CruxAdapter ConsensusMapNormalizer QCShrinker QCImporter SpectraFilterScaler IDExtractor QCExtractor ProteinResolver LowMemPeakPickerHiRes LowMemPeakPickerHiResRandomAccess MT2MQ PepQuery MyriMatch idpEmbedder idpQonvert idpAssemble PyProphet export moFF Unipept PyProphet score Kronik Hardklor diapysef library generation PyProphet merge PyProphet peptide PyProphet protein PyProphet subsample Proteinortho summary Proteinortho grab proteins Proteinortho FlashLFQ QuantWiz-IQ Peptide Genomic Coordinate Pathway Matcher Peptide Shaker Raw Tools DIA_Umpire_SE CustomProDB QuanTP Search GUI PepPointer megahit contig2fastg Search engine output to Pin converter Percolator Pout2mzid Create nested list Label free protein MS-GF+ Protease prediction Calculate protein properties RTPredict PTPredict InspectAdapter InclusionExclusionListCreator LowMemPeakPickerHiResRandomAccess IDDecoyProbability RNPxl AdditiveSeries TopPerc Protease prediction Create Decoy Database (reverse) Morpheus FastaCLI Identification Parameters Diffacto ProteomIQon MzMLToMzLite ProteomIQon PeptideDB ProteomIQon PeptideSpectrumMatching ProteomIQon PSMStatistics ProteomIQon ProteinInference Validate FASTA Database Proteomiqon PSMBasedQuantification Proteomiqon JoinQuantPepIonsWithProteins Proteomiqon LabeledProteinQuantification Proteomiqon LabelFreeProteinQuantification TRIC X!Tandem MSMS Search MSI single ion segmentation MSI colocalization MetaNovo prot-scriber syndiva X!Tandem MSMS Search

Metabolomics

MetFrag Align Samples Replicate Filter Process Scans (and SIM-Stitch) MetFrag Vis Get peaklists Convert DIMSpy-based HDF5 to tsv Missing Values Sample Filter Sample Filter Blank Filter SIRIUS-CSI:FingerID msPurity.spectralMatching msPurity.purityX msPurity.dimsPredictPuritySingle Merge peaklists msPurity.createMSP msPurity.createDatabase msPurity.averageFragSpectra msPurity.filterFragSpectra msPurity.frag4feature msPurity.purityA msPurity.flagRemove W4m Data Subset Heatmap genform NMR_Annotation xcms get a sampleMetadata file Table Merge Intensity Check ID choice Normalization mixmodel ASCA Between-table Correlation HMDB MS search bank_inhouse LCMS matching Golm Metabolome Database search spectrum NMR_Preprocessing NMR_Read xcms process history CAMERA.annotate xcms fillChromPeaks (fillPeaks) xcms adjustRtime (retcor) xcms groupChromPeaks (group) xcms findChromPeaks Merger xcms plot chromatogram xcms findChromPeaks (xcmsSet) MSnbase readMSData Lipidmaps OPLS-DA_Contrasts Join +/- Ions Generic_Filter Quality Metrics metaMS.runGC Multilevel Check Format Determine_batch_correction Batch_correction MassBank spectrum searches ProbMetab Tool CAMERA.combinexsAnnos proFIA NMR_Bucketing NMR_Normalization NMR spectra alignment NMR spectra alignment xcms refineChromPeaks (refine) Isoplot: Generate plots from isocor output

ChemicalToolBox

Alphafold 2 Generate MD topologies for small molecules Search ChEMBL database AnteChamber Convert Parameters ParmChk2 MMPBSA/MMGBSA GROMACS solvation and adding ions GROMACS structure configuration Create GROMACS index files Create GROMACS position restraints files Extract energy components with GROMACS Modify/convert and concatate GROMACS trajectories GROMACS simulation GROMACS energy minimization GROMACS initial setup Substructure Search Hierarchical clustering Extract clusters of MD trajectories Extract RMSD distance matrix data Add hydrogen atoms Remove counterions and fragments ChEMBL structure pipeline dcTMD friction correction Remove protonation state Ramachandran Analysis End-to-End Analysis Cosine Content Hydrogen Bond Analysis Ramachandran Plots Distance Analysis Dihedral Analysis OpenPepXL Change title RDF Analysis Spectrophores search Angle Analysis APoc smina Prepare receptor Enumerate changes Extract values from an SD-file fpocket Calculate molecular descriptors PubChem Download PubChem Assay Downloader VINA Docking Prepare ligand Calculate the box parameters using RDKit Remove duplicated molecules Filter Compound conversion Visualisation Compute physico-chemical properties Compound search Remove small molecules Prepare ligands for docking Descriptors Drug-likeness Score docked poses using SuCOS Cluster ligands using SuCOS Max SuCOS score Determine distance to defined points Create Frankenstein ligand rDock cavity definition rDock docking rDock docking rxDock cavity definition rxDock docking SDF sort and filter Calculate plane of best fit for molecules Reaction SMARTS filter Generate conformers Constrained conformer generation Butina Cluster Matrix Open 3D Align Standardize SD-files Butina Cluster Pick Reaction maker Screen XCos ‘FeatureStein’ fragment overlay scoring Merge GROMACS topologies OpenDUck chunk Run OpenDUck XChem TransFS pose scoring Molecule to fingerprint NxN clustering Taylor-Butina clustering SDF to Fingerprint MDTraj file converter fastpca RDConf: Low-energy ligand conformer search Trajectory select and merge Alchemical Analysis Hydrogen Bond Analysis using VMD PCA visualization RMSF Analysis PCA RMSD Analysis DCCM analysis Slice MD trajectories PACKMOL PaDEL descriptor Online data Get PDB file Multi Compound Search Remove counterions and fragments Substructure Search Multi Compound Search Spectrophores(TM) search: Molecule recognition Natural Product Similarity Search Conformer calculation MDS Scatter Plot Online data Fragmenter PubChem Assay Downloader Merging Open Molecule Generator ChEMBL structure pipeline GROMACS production simulation Pharmacophore alignment Pharmacophore dpocket GROMACS Radius of Gyration Convert Amber topology and coordinate files to GROMACS format Build tLEaP Adding New Topology Information Extracting Topology Information GROMACS copy file PDBFixer GROMACS check GROMACS RMSD calculation GROMACS RMSF calculation

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Statistics and Visualisation

Statistics

MINE Draw ROC plot Perform LDA Generate A Matrix Count GFF Features Correlation Perform Best-subsets Regression Principal Component Analysis Kernel Principal Component Analysis Kernel Canonical Correlation Analysis Canonical Correlation Analysis T Test for Two Samples Sparse Matrix Functions Create a model to recommend tools Wavelet variance GraphEmbed Landmark Registration Plot actual vs predicted curves and residual plots Plot confusion matrix, precision, recall and ROC and AUC curves Rolling window Nearest Neighbors Classification Support vector machines (SVMs) Anova Multivariate Univariate IWTomics Plot with Threshold IWTomics Test IWTomics Load Sequence composition Biosigner Transformation Heatmap RGCCA Statistical hypothesis testing Summary Statistics Count

Machine Learning

Principal component analysis LightGBM Numeric Clustering Stacking Ensembles Deep learning training and evaluation Machine Learning Visualization Extension Support vector machines (SVMs) Train, Test and Evaluation Model Prediction Generate Estimator attributes Hyperparameter Search Pipeline Builder Evaluate pairwise distances Nearest Neighbors Classification Ensemble methods Feature Selection Preprocess Calculate metrics Calculate metrics Discriminant Analysis Generalized linear models Model Validation Evaluate a Fitted Model Fit a Pipeline, Ensemble Split Dataset Build Deep learning Batch Training Models Create deep learning model Create a deep learning model architecture Sparse Matrix Functions Create a model to recommend tools virhunter To categorical MCL decontaminator

Graph/Display Data

heatmap2 Build custom track Scatterplot Histogram GMAJ Plotting tool BAM Coverage Plotter JBrowse - Data Directory to Standalone JBrowse pyGenomeTracks Circos: Interval to Tiles Circos: Resample 1/2D data Circos: Link Density Track Circos: bigWig to Scatter Circos: Interval to Circos Text Labels Circos: Alignments to links Circos: Table viewer Circos GC Skew Circos: Stack bigWigs as Histogram Circos: Bundle Links Heatmap w ggplot Violin plot w ggplot2 Scatterplot with ggplot2 Histogram with ggplot2 Plot confusion matrix, precision, recall and ROC and AUC curves Newick Display Bandage Info Bandage Image UpSet diagram Pairwise intersection Krona pie chart Pathview Export to GraPhlAn Venn Diagram Volcano Plot Plot actual vs predicted curves and residual plots Parallel Coordinates Plot PCA plot w ggplot2 Fasta nucleotide color plot GraPhlAn Generation, personalization and annotation of tree rtsne Visualize with Krona Fasta nucleotide color plot MUMmer dotplot Karyotype Plotting tool Paired-end histogram Pretext Snapshot Bar chart Pathifier Boxplot VCF to MAF Custom Track

Muon Spectroscopy

PyMuonSuite AIRSS Cluster PyMuonSuite AIRSS DFTB+ Optimise PyMuonSuite AIRSS UEP Optimise PyMuonSuite AIRSS Generate PyMuonSuite Phonons MuSpinSim Simulate cif2cell MuSpinSim Configure MuSpinSim Plot PyMuonSuite Symmetry PyMuonSuite AIRSS Configure

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Miscellaneous Tools

Evolution

Mutate Codons IQ-TREE codeML Structure Join neighbors TN93 TN93 Filter TN93 Cluster Merge matching reads aaChanges phyloP

Motif Tools

Sequence Logo MEME psp-gen FIMO MEME DREME MEME-ChIP

Test Tools

ChIPpeakAnno annoPeaks Cluster Profiler Bitr Cluster Profiler GO hifive instaGRAAL PyIron Personal Cancer Genome Reporter Tombo Re-squiggle Tombo create Tombo detect modifications Tombo plot most signficant Tombo plot genome locations Peptide Prophet Protein Prophet InterProphet Discriminant Analysis Convert Transform Nearest Neighbors Classification Numeric Clustering Support vector machines (SVMs) Sparse Matrix Functions Preprocess Evaluate pairwise distances Generate Ensemble methods Calculate metrics Protease prediction bwtool-lift Calculate protein properties Base Count Codon count GenBank and EBML Extract sequences from GenBank GFF converter Sequence converter Translate nucleotides RNALfoldz HE/ MALDI Image Registration

GIS Data Handling

NetCDF xarray Metadata Info NetCDF xarray Selection OGR Informations OGR2ogr GDAL Warp GDAL Translate GDAL Merge GDAL Informations GDAL Build VRT GDAL addo NetCDF xarray operations NetCDF xarray map plotting NetCDF xarray Coordinate Info

Animal Detection on Acoustic Recordings

Get species occurrences data Advanced restitution: ‘Point fixe’ protocol Advanced restitution: ‘Routier’or ‘Pedestre’ protocols Tadarida data cleaner Tadarida identifications validation

Compute indicators for satellite remote sensing

Compute a PCA raster Map diversity Preprocess sentinel 2 data Compute spectral indices Compare diversity indicators Compute biodiversity indices Validate ISO 19139

Regional Variation

Fetch Indels Draw Stacked Bar Plots Delete Overlapping Indels Compute Motif Frequencies Compute Motif Frequencies For All Motifs Categorize Elements Feature coverage

Genome Diversity

FASTTREE Make File Specify Individuals Nucleotide Diversity Founders sequenced Matings Phylogenetic Tree Admixture Phylip Diversity Draw variants Remarkable Intervals Differential Cleavage Reorder individuals Pairs sequenced Inbreeding and kinship Ancestry Population Complexity Prepare Input Aggregate Individuals RAxML Phyogenetic reconstruction with RAxML gd_snp to VCF Overall FST Pathway Image Close relatives PCA Filter SNPs Coverage Distributions Pick Primers Flanking Sequence Rank Pathways Per-SNP FSTs Sample SNPs Restore Attributes Convert Rank Terms Get Pathways Cluster KEGG

Climate Analysis

CTSM/FATES-EMERALD climate stripes map plot Copernicus Essential Climate Variables zonal statistics shift longitudes Copernicus Climate Data Store CESM Copernicus Atmosphere Data Store EODIE CDO Operations CDO get info NetCDF timeseries Extractor

Apollo

Delete all annotations from an Apollo record List Organisms Register Account Delete an Apollo record Create or Update Organism Annotate Retrieve Data GFF3 to Apollo Annotations Retrieve JBrowse

Imaging

CellProfiler Starting Modules ColorToGray Tile TrackObjects OverlayOutlines ConvertObjectsToImage DisplayDataOnImage EnhanceOrSuppressFeatures ExportToSpreadsheet GrayToColor IdentifyPrimaryObjects MaskImage MeasureGranularity MeasureImageAreaOccupied MeasureImageIntensity MeasureImageQuality MeasureObjectIntensity MeasureObjectSizeShape MeasureTexture RelateObjects SaveImages ImageMath Image Registration Projective Transformation SpyBOAT Convert binary image to EDM Skeletonize Find edges Add shadow effect Enhance contrast Find maxima Watershed segmentation Apply raw transformation Operate on pixels Apply elastic transformation IDR/OMERO Download Extract top view GeneSeqToFamily preparation Image Converter Landmark Registration Adapt an elastic transformation Adjust threshold Compose two elastic transformations Sharpen Convert to binary Convert elastic transformation to raw Compare two raw deformations Compare opposite elastic deformations Analyze skeleton Smooth Align two images Compose two raw transformations Add or remove noise Create new image Analyze particles Compose a raw and an elastic transformation Compare elastic and raw deformation Image Info Detection Visualization Local Threshold Auto Threshold Histogram equalization Convert image 2D Feature Extraction Permutate image Label to Points Points to Label Concatenate images Scale Image Merge Neighbours in Label Binary 2 Label Filter segmentation Split objects Anisotropic Diffusion Color Deconvolution Filter Image Points to Label Switch axis coordinates Coordinates of ROI Count Objects Mahotas-features Points to Binary Image Projective Transformation Visceral Binary To Points Slice Image Split Labelmap Curve Fitting Association of points Spot Detection Overlay Images CellProfiler SegMetrics Gate Finder Vitessce Visualization Squidpy Graph and Plotting Rename OME-TIFF Channels Process single-cell intensities Mesmer

Species abundance

Compute GLM on population data Compute GLM on community data Temporal trend indicator Estimate temporal population variation Estimate temporal population variation Filter species Preprocess population data NetCDF xarray Metadata Info NetCDF xarray Selection Calculate community metrics Calculate presence absence table Create a plot from GLM data Model temporal trend Flight curve Autocorrelation test Expected temporal trend Linear regression ajusted Plot abundance Abundance index

Compute indicators for turnover boulders fields

QECB-Dissimilarity IVR Diversity

Interactive tools

Pavian Interactive MGnify Notebook Interactive JupyTool and notebook GPU enabled Interactive Jupyter Notebook for Machine Learning Interactive Climate Notebook Interactive Pangeo Notebook RStudio PyIron Interactive Jupyter Notebook HiGlass OpenRefine Ubuntu XFCE Desktop Panoply AskOmics Interactive CellXgene Environment bam.iobio visualisation VCF (iobio) Visualisation Neo4j (Graph Database) Phinch Visualisation Paraview Wilson Wallace geoexplorer radiant EtherCalc VRM Editor SimText iSEE metashark

OBO Ontology manipulation

Get the ancestor terms of a given OBO term Get all the relationship types Convert OBO to RDF Get the parent terms Get the terms Get all terms Convert OBO to OWL Get all the relationship IDs and namespaces Get all term synonyms Get the descendent terms Get all the term IDs and term names Get child terms Get subontology Get all the relationship IDs and definitions Get the terms that are related Get the root terms Get all the relationship IDs and names

HCA-Single Cell

Scanpy FindMarkers Scanpy ScaleData Scanpy RunUMAP Scanpy RunTSNE Scanpy RunPCA Scanpy Read10x Scanpy NormaliseData Scanpy FindVariableGenes Scanpy FindCluster Scanpy FilterGenes Scanpy FilterCells Scanpy ComputeGraph Human Cell Atlas Matrix Downloader GTF2GeneList UCSC Cell Browser Scanpy ParameterIterator Scanpy PlotTrajectory Scmap index cells EBI SCXA Data Retrieval

Other Tools

Get PubMed abstracts Text to wordmatrix PMIDs to PubTator PubMed query SPRING Cross SPRING Model-All DBKit Create SPRING Map SPRING Min-Z SPRING Model SPRING MCC DBKit Extract DBKit Merge

Biodiversity data exploration

Diversity Ocean biodiversity indicators Spatial coordinates anonymization Local Contributions to Beta Diversity (LCBD) Homoscedasticity and normality Variables exploration Presence-absence and abundance Statistics on presence-absence

Sanger Sequencing

tracy Basecall tracy Align tracy Decompose tracy Assemble

Extract Features

Gene length and GC content Parse mitochondrial blast ORFipy b2bTools: Biophysical predictors for single sequences

Metagenomic Analysis

Summarize taxonomy Draw phylogeny Poisson two-sample test Find lowest diagnostic rank Fetch taxonomic representation Find diagnostic hits

GATK Tools

Count Covariates

QIIME 2

qiime2 deblur denoise-16S qiime2 tools export qiime2 vsearch uchime-ref qiime2 vsearch uchime-denovo qiime2 vsearch fastq-stats qiime2 vsearch cluster-features-de-novo qiime2 taxa filter-table qiime2 taxa barplot qiime2 sample-classifier summarize qiime2 sample-classifier split-table qiime2 sample-classifier regress-samples-ncv qiime2 sample-classifier regress-samples qiime2 sample-classifier predict-regression qiime2 sample-classifier predict-classification qiime2 sample-classifier metatable qiime2 sample-classifier fit-regressor qiime2 sample-classifier fit-classifier qiime2 sample-classifier confusion-matrix qiime2 sample-classifier classify-samples-from-dist qiime2 quality-filter q-score qiime2 quality-control filter-reads qiime2 quality-control evaluate-seqs qiime2 quality-control bowtie2-build qiime2 phylogeny filter-table qiime2 phylogeny fasttree qiime2 phylogeny align-to-tree-mafft-fasttree qiime2 metadata shuffle-groups qiime2 metadata distance-matrix qiime2 longitudinal pairwise-distances qiime2 longitudinal pairwise-differences qiime2 longitudinal linear-mixed-effects qiime2 longitudinal first-distances qiime2 longitudinal first-differences qiime2 longitudinal feature-volatility qiime2 longitudinal anova qiime2 gneiss ilr-phylogenetic-ordination qiime2 gneiss ilr-phylogenetic qiime2 gneiss dendrogram-heatmap qiime2 gneiss correlation-clustering qiime2 fragment-insertion sepp qiime2 feature-table transpose qiime2 feature-table tabulate-seqs qiime2 feature-table subsample qiime2 feature-table rename-ids qiime2 feature-table rarefy qiime2 feature-table presence-absence qiime2 feature-table merge-taxa qiime2 feature-table merge qiime2 feature-table group qiime2 feature-table filter-seqs qiime2 feature-table filter-samples qiime2 feature-table filter-features qiime2 feature-table core-features qiime2 feature-classifier vsearch-global qiime2 feature-classifier fit-classifier-sklearn qiime2 feature-classifier find-consensus-annotation qiime2 feature-classifier extract-reads qiime2 feature-classifier classify-sklearn qiime2 feature-classifier classify-hybrid-vsearch-sklearn qiime2 feature-classifier blast qiime2 emperor biplot qiime2 diversity-lib unweighted-unifrac qiime2 diversity-lib pielou-evenness qiime2 diversity-lib observed-features qiime2 diversity-lib bray-curtis qiime2 diversity-lib beta-phylogenetic-meta-passthrough qiime2 diversity-lib alpha-passthrough qiime2 diversity tsne qiime2 diversity procrustes-analysis qiime2 diversity mantel qiime2 diversity core-metrics-phylogenetic qiime2 diversity core-metrics qiime2 diversity bioenv qiime2 diversity beta-rarefaction qiime2 diversity beta-group-significance qiime2 diversity alpha-rarefaction qiime2 diversity alpha-phylogenetic qiime2 diversity alpha-group-significance qiime2 diversity alpha qiime2 demux subsample-single qiime2 demux subsample-paired qiime2 demux emp-single qiime2 deblur visualize-stats qiime2 dada2 denoise-single qiime2 dada2 denoise-ccs qiime2 cutadapt demux-single qiime2 composition ancombc qiime2 composition add-pseudocount qiime2 alignment mask qiime2 alignment mafft qiime2 composition ancom qiime2 composition tabulate qiime2 cutadapt demux-paired qiime2 cutadapt trim-paired qiime2 cutadapt trim-single qiime2 dada2 denoise-paired qiime2 dada2 denoise-pyro qiime2 deblur denoise-other qiime2 demux emp-paired qiime2 demux filter-samples qiime2 demux summarize qiime2 diversity adonis qiime2 diversity alpha-correlation qiime2 diversity beta qiime2 diversity beta-phylogenetic qiime2 diversity beta-correlation qiime2 diversity filter-distance-matrix qiime2 diversity pcoa qiime2 diversity pcoa-biplot qiime2 diversity umap qiime2 diversity-lib beta-passthrough qiime2 diversity-lib beta-phylogenetic-passthrough qiime2 diversity-lib faith-pd qiime2 diversity-lib jaccard qiime2 diversity-lib shannon-entropy qiime2 diversity-lib weighted-unifrac qiime2 emperor plot qiime2 emperor procrustes-plot qiime2 feature-classifier classify-consensus-blast qiime2 feature-classifier classify-consensus-vsearch qiime2 feature-classifier fit-classifier-naive-bayes qiime2 feature-table filter-features-conditionally qiime2 feature-table heatmap qiime2 feature-table merge-seqs qiime2 feature-table summarize qiime2 feature-table relative-frequency qiime2 fragment-insertion classify-otus-experimental qiime2 fragment-insertion filter-features qiime2 gneiss assign-ids qiime2 gneiss gradient-clustering qiime2 gneiss ilr-hierarchical qiime2 gneiss ilr-phylogenetic-differential qiime2 longitudinal maturity-index qiime2 longitudinal nmit qiime2 longitudinal plot-feature-volatility qiime2 longitudinal volatility qiime2 metadata tabulate qiime2 phylogeny align-to-tree-mafft-iqtree qiime2 phylogeny filter-tree qiime2 phylogeny iqtree qiime2 phylogeny iqtree-ultrafast-bootstrap qiime2 phylogeny midpoint-root qiime2 phylogeny raxml qiime2 phylogeny raxml-rapid-bootstrap qiime2 phylogeny robinson-foulds qiime2 phylogeny align-to-tree-mafft-raxml qiime2 quality-control evaluate-composition qiime2 quality-control evaluate-taxonomy qiime2 quality-control exclude-seqs qiime2 sample-classifier classify-samples qiime2 sample-classifier classify-samples-ncv qiime2 sample-classifier heatmap qiime2 sample-classifier scatterplot qiime2 taxa collapse qiime2 taxa filter-seqs qiime2 vsearch cluster-features-closed-reference qiime2 vsearch cluster-features-open-reference qiime2 vsearch merge-pairs qiime2 vsearch dereplicate-sequences qiime2 tools import qiime2 alignment mafft-add

Built-in Converters

Convert compressed file to uncompressed. Convert compressed file to uncompressed. OpenBabel converter for molecular formats Convert plink pbed to linkage lped Convert Genomic Intervals To Strict BED6 Convert MOL2 to MOL Convert uncompressed file to compressed Convert BED, GFF, or VCF to BigWig Convert FASTQ files to seek locations Convert XTC, DCD, and TRR Convert BAM to queryname-sorted BAM Convert InChI to MOL Convert Interval to BGZIP Convert PDB to GRO Convert BED to GFF Convert Genomic Intervals To Strict BED Convert Len file to Linecount Convert SAM to BigWig Convert compressed and uncompressed BCF files Convert Wiggle to BigWig Convert Interval to tabix Convert MAF to Fasta Convert Genomic Intervals To BED Convert Wiggle to Interval Convert BAM to coordinate-sorted BAM Convert plink pbed to ld reduced format Convert BAM to BigWig Convert CML to SMILES Convert MAF to Genomic Intervals Convert Parquet to csv Convert GRO to PDB Convert lped to fped Convert Genomic Intervals To Strict BED12 Convert BGZ VCF to tabix Convert Bam to Bai Convert BigWig to Wiggle Convert tabular to CSV Convert CRAM to BAM Convert Ref taxonomy to Seq Taxonomy Convert SMILES to MOL Convert FASTA to Bowtie color space Index Convert Biom datasets Convert tabular to dbnsfp Convert Picard Interval List to BED6 Convert Genomic Intervals To Coverage Convert GFF to Interval Index Convert GFF to Feature Location Index Convert FASTA to len file Convert FASTA to Tabular Convert SAM to BAM without sorting Convert neostore.zip files to neostore Convert GFF to BED Convert FASTA to 2bit Convert BED to Feature Location Index SMILES to SMILES Convert CSV to tabular Convert lped to plink pbed Convert tar to directory Convert FASTA to Bowtie base space Index Convert BedGraph to BigWig Convert FASTA to fai file