European Galaxy Tools

Adds environment variables AquaINFRA Importer Argo data access BioMart BioMart CBI Rice Mart Copernicus Marine Data Store DICED Database DoRiNA Search Download and Extract Reads in BAM Download and Extract Reads in FASTQ Download and Generate Pileup Format Download run data EBI SRA EBI Search EGA Download Client Enrich dataset with WoRMS EuPathDB Faster Download and Extract Reads in FASTQ Flymine Get Microbial Data Get features by Ensembl ID Get gene tree by Ensembl ID Get sequences by Ensembl ID Get species occurrences data GrameneMart HbVar IEDB IMPC InterMine MaveDB MouseMine NCBI Accession Download NCBI Datasets Gene NCBI Datasets Genomes NCBI Datasets Genomes NCBI ECitMatch NCBI EFetch NCBI EGQuery NCBI EInfo NCBI ELink NCBI EPost NCBI ESearch NCBI ESummary NFDI4Earth OneStop4All Importer OBIS occurences OmicsDI OpenAlex explorer Protein Database Downloader Ratmine Retrieve ENA data Retrieve ENA taxon data Retrieve a run report Retrieve an analysis report Retrieve bold SEEK test SRA SdmPredictors List Layers Search ENA data UCSC Archaea UCSC Main UniProt Unipept Upload File WormBase Xarray Import Data YeastMine ZebrafishMine downloads fastq-dl metabolicMine modENCODE fly modENCODE modMine modENCODE worm pysradb search

ENA Upload tool ENA Webin CLI Export datasets cURL

Apply rules Build list Collapse Collection Column join Convert sample sheet Duplicate file to collection Extract dataset Extract element identifiers Filter collection Filter empty datasets Filter failed datasets Filter null elements Flat Cross Product Flatten collection Harmonize two collections Keep success Merge collections Nest collection Nested Cross Product Pick parameter value Relabel identifiers Sample sheet to tabular Sort collection Split Paired and Unpaired Split file Split file Tag elements Unzip Unzip collection Zip collections

Calculate numeric parameter value Compose text parameter value Map parameter value Parse parameter value Parse value from image metadata

Add column Add column Add input name as column Add line to file Advanced Cut Arithmetic Operations Change Case Column Regex Find And Replace Compute Concatenate datasets Concatenate multiple datasets or collections Convert Coverage Create single interval Create text file Cut Excel to Tabular Fetch closest non-overlapping feature Filter Tabular Get flanks Histogram Intersect Join Join datasets by identifier column Join two files Line/Word/Character count Merge Merge Columns Multi-Join Number lines Paste Query Tabular Rebase GFF3 features Regex Find And Replace Regex Replace Regex switch Remove beginning Remove columns Replace Replace Text Replace Text Replace chromosome names Replace column SQLite to tabular Search in textfiles Secure Hash / Message Digest Select first Select first Select last Select last Select random lines Sort Sort Column Order Sort a row Split by group Subtract Whole Dataset Switch axis coordinates Table Compute Text file format converters (dos2unix) Text reformatting Text transformation Trim Unfold Unique Unique Unique lines cast diff jq melt tac

AGAT BAM BED GFF coverage bigWigs BED-to-GFF BED-to-bigBed Convert Glimmer to GFF Convert a 10X BAM file to FASTQ Convert image format FFmpeg Format Converter GFF-to-BED MAF to BED MAF to FASTA MAF to Interval Markitdown SFF converter Table to GeoJSON wigtobigwig

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

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

(CPT) Genbank to GFF3: AXT to FASTA AXT to LAV AXT to concatenated FASTA Add metadata BED-to-GFF BED-to-bigBed Compare two images Compress file(s) Convert Convert BAM Convert BAM to ScIdx Convert GTF to BED12 Convert Glimmer to GFF Convert genome coordinates Convert gffCompare annotated GTF to BED Convert image format Create InterMine Interchange Create a BIOM table CrossMap BAM CrossMap BED CrossMap BigWig CrossMap GFF CrossMap VCF CrossMap Wig CrossMap region Extract MAF blocks FASTA-to-Tabular FFmpeg Format Converter Fix tRNA model GFA to FASTA GFF-to-BED GFF3 to GenBank GTF-to-BEDGraph Genbank to Five Column Format Image Montage LAV to BED MAF to BED MAF to FASTA MAF to Interval MGA to GFF3 Map peptides to a bed file Markitdown Normalize PacBio bam2fastx Resize coordinate window SFF converter Split GFF3+Fasta into separate parts Stitch Gene blocks Subset Summarize sample or observation data Table to GeoJSON Thermo ToolDistillator ToolDistillator Summarize UniProt Wiggle-to-Interval ab1 to FASTQ converter axtChain axtToMaf bax2bam bed to protein map bigWigToBedGraph chainAntiRepeat chainNet gffread hictk idconvert idconvert idpQuery mafToAxt msconvert msconvert Subset Peak List msms_extractor mz to sqlite netFilter netToAxt samtools BAM to CRAM twoBitToFa wigtobigwig xmlstarlet

ART 454 ART Illumina ART SOLiD AdapterRemoval: remove adapter sequences AmpliGone BBTools: BBMerge BBTools: BBNorm BBTools: BBduk BBTools: Tadpole Barcode Splitter Barcode Splitter Berokka Build base quality distribution CIAlign Calculate sequence complexity Clip Collapse Collector’s curve Combine FASTA and QUAL Compute quality statistics Compute quality statistics Compute sequence length Concatenate Convert Create binary barcodes Cutadapt Draw nucleotides distribution chart Draw quality score boxplot Draw quality score boxplot Exonerate Extract alignment ends Extract barcodes Extract nanopore events FASTA Merge Files and Filter Unique Sequences FASTA Width FASTA-to-Tabular FASTQ Groomer FASTQ Masker FASTQ Quality Trimmer FASTQ Summary Statistics FASTQ Trimmer FASTQ de-interlacer FASTQ interlacer FASTQ joiner FASTQ splitter FASTQ to FASTA FASTQ to FASTA FASTQ to Tabular FASTQE FLASH Faffy chunk Faffy extract Faffy merge Falco FastQC Fasta Statistics Fasta regular expression finder Fastplong Fastq groupmerge Filter FASTQ Filter by quality Filter sequences by length Filter sequences by mapping Generate box-whisker Generate histogram Get crosslinked nucleotides Je-Clip Je-Demultiplex Je-Demultiplex-Illu Je-MarkDuplicates Length Distribution Manipulate FASTQ Merge PCR duplicates Merging paired-end Illumina reads (SeqPrep) NCBI FCS GX PRINSEQ Pear Plot performance Plot signals Quality format converter RNA-seq Rcorrector RNA/DNA RRM-Scorer Remove 3’-end nts Remove Description Remove sequencing artifacts Remove spurious Rename sequences Reverse-Complement Select high quality segments SeqKit Head SeqKit fx2tab SeqKit grep SeqKit locate SeqKit sort SeqKit statistics SeqKit translate Seqkit Split2 Sickle Split Fasta Tabular to FASTQ Tabular-to-FASTA Thread nucleotides onto a protein alignment (back-translation) Trim Galore! Trim putative adapter sequence Trim sequences Trimmomatic UMI-tools count UMI-tools deduplicate UMI-tools extract UMI-tools group UMI-tools whitelist faSplit fastp fastq-join filtlong gfastats lighter mQC qfilt rasusa rdeval rdeval report seqtk_comp seqtk_cutN seqtk_dropse seqtk_fqchk seqtk_hety seqtk_listhet seqtk_mergefa seqtk_mergepe seqtk_mutfa seqtk_randbase seqtk_sample seqtk_seq seqtk_subseq seqtk_telo seqtk_trimfq

Mt/Nuc Ratio Calculator Preseq c_curve Preseq lc_extrap

FASTQ info File Format Identification MultiQC QualiFilter QualiMap Counts QC sequali

Analysis of artifacts with Tasmanian BAM filter BamHash BamUtil clipOverlap BamUtil diff Convert SAM Cramino Filter BAM Filter SAM or BAM, output SAM or BAM Filter pileup Generate pileup NuDUP Operate on and transform BAM Panel Coverage Report Pileup-to-Interval QualiMap BamQC QualiMap Multi-Sample BamQC RmDup Sambamba flagstat Sambamba markdup Sambamba merge Sambamba sort Samtools ampliconclip Samtools bedcov Samtools calmd Samtools collate Samtools consensus Samtools coverage Samtools depth Samtools fastx Samtools fixmate Samtools flagstat Samtools idxstats Samtools markdup Samtools merge Samtools mpileup Samtools phase Samtools reheader Samtools sort Samtools split Samtools stats Samtools view Slice Split Split BAM by read tag value Split BAM by reads mapping status Split BAM by reference Split BAM into paired- and single-end Tag pileup frequency mosdepth revertR2orientationInBam samblaster

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

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

Chopper Clair3 CoNvex Collector’s curve Extract FASTQ Extract nanopore events Extract reads Extract time FLAIR collapse FLAIR correct Generate box-whisker Generate histogram Get longest read NanoComp NanoComporeDB NanoFilt NanoPlot Nanopolish eventalign Nanopolish methylation Nanopolish polyA Nanopolish variants NanopolishComp: EventalignCollapse NanopolishComp: FreqMethCalculate Plot performance Plot signals Porechop Pycoqc Read length statistics SampComp Show nucleotide Show quality m6anet medaka consensus pipeline medaka inference tool medaka variant pipeline medaka vcf tool ont_fast5_api: Compress ont_fast5_api: Multi to single ont_fast5_api: Single to multi ont_fast5_api: Subset

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

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

ABRicate ABRicate List ABRicate Summary ACGT Content AEGeAn CanonGFF3 AEGeAn GAEVAL AEGeAn LocusPocus AEGeAn ParsEval AGAT AMRFinderPlus ANGSD ANGSD X-Contamination Annotate with DGI Annotate with DGI Annotation Table Antismash Augustus BRAKER3 Bakta Beta Diversity BlastXML to gapped GFF3 Braker genome annotation Build a GeneNoteBook Busco CPAT Categorize ChIPseeker ChewBBACA AlleleCall Commet Compare BIOM tables Compute Convert GFF3 Convert XMFA to gapped GFF3 Converts GTF to Annotations file for Homer CoreProfiler allele_calling Create binary barcodes CryptoGenotyper DRHIP DeepARG predict DeepARG short reads DeepSig Detect circular sequences DiscoSnp++ DiscoSnpRAD DotKnot EVidenceModeler Embed Query Sequences EndorSpy Exonerate Extract ORF Extract alignment ends Extract barcodes Extract sequence regions FastANI FastOMA Fasta Translate Filter with SortMeRNA Find Nested Alternate ORFs (nAlt-ORFs) Format Funannotate assembly clean Funannotate compare Funannotate functional Funannotate predict annotation GECCO GFF3 Add Gene to CDS GFF3 Add Gene to CDS for Sixpack GFF3 Feature Sequence Export GFF3 Feature Type Filter GFF3 Filter: Require Phage Start GOEnrichment GOSlimmer Genbank to GFF3 Genome Editor Genome annotation statistics Get Codon and Bicodon frequency Get Codon frequency Get crosslinked nucleotides Get open reading frames (ORFs) or coding sequences (CDSs) Gff3 Filter: Require SD GffCompare Glimmer ICM builder Glimmer long ORFs Glimmer3 Glimmer3 Glimmer3 to GFF3 GotohScan Groot Gubbins HHsearch Helixer HiCap ICEscreen ISEScan Identify Lipoboxes Integron Finder InterProScan Interrupted gene detection tool Intersect and Adjacent KOBAS Annotate KOBAS Identify KisSplice KofamScan LC/MS matching Liftoff List spaln parameter tables MITOS MITOS2 MLST MLST List MMseqs2 easy-cluster MMseqs2 easy-linsearch MMseqs2 easy-rbh MMseqs2 easy-search MMseqs2 easy-taxonomy MMseqs2 taxonomy MOB-Recon MOB-Typer Maker Map annotation ids Mapsembler2 Meningotype Metagenome Contributions Minimap2-inferred sequence typing (MiST) call Minimap2-inferred sequence typing (MiST) dists Miniprot align Miniprot index MirMachine NCBI EGAPx NCBI FCS Adaptor Neighbors Nucleosome Predictions Nucleotide subsequence search OMArk OptiType OrthoFinder PIRATE PPanGGOLiN MSA PPanGGOLiN all PPanGGOLiN projection PPanGGOLiN rarefaction PSORTb PanTA Panaroo PfamScan Phage QC PlasClass PlasmidFinder Predict Metagenome Prep GFF3 Input for Apollo ProbMetab Tool Prodigal Gene Predictor Prokka Promoter 2.0 Protein Blast Grouping Psauron RXLR Motifs Reassign reads Rebase GFF3 features Reconstruct haplotypes Red Related Prophages tool Remove 3’-end nts Remove Annotation Feature Remove terminal stop codons Renumber GenBank Genes RepeatExplorer (clustering) RepeatMasker RepeatModeler Roary SNAP STR to bed Sanntis biosynthetic gene clusters Sex.DetERRmine Shine Find SignalP 3.0 SnpSift GeneSets Sort assembly Spaln: align cDNA or Protein to genome SpoTyping TAPScan Classify TB Variant Filter TB Variant Report TB-Profiler Collate TB-Profiler Profile TB-Profiler Profile TETyper TEfinder TMHMM 2.0 TRANSIT Gumbel TRANSIT HMM TRANSIT Resampling TRANSIT Tn5Gaps TSEBRA Table to GFF3 TakeABreak Telogator Telogator Make Reference Tiberius Train Augustus Train SNAP TransTermHP UCSC BLAT Alignment Tool WindowMasker mkcounts WindowMasker ustat WoLF PSORT abriTAMR add-read-counts alimask annotateMyIDs annotatePeaks argNorm autoBIGS.cli chewBBACA AlleleCallEvaluator chewBBACA CreateSchema chewBBACA DownloadSchema chewBBACA ExtractCgMLST chewBBACA JoinProfiles chewBBACA NSStats chewBBACA PrepExternalSchema compleasm ectyper edta estimate-energy extract-boxed-sequences fargene fgsea filter-annotated-entries filter-by-energy find-boxes findMotifs findMotifsGenome fix-fasta-headers gProfiler Convert gProfiler GOSt gProfiler Orth gProfiler Random gProfiler SNPense goseq hAMRonize hamronize summarize: hicBuildMatrixMicroC hicstuff full pipeline hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmscan hmmsearch jackhmmer krocus legsta longdust lorikeet spoligotyping mafFilter miRanda mkyrobe predict multiGSEA netboxr nhmmer nhmmscan pharokka phmmer progressiveMauve psortb scanMotifGenomeWide segmentation-fold seq2HLA sistr_cmd socru staramr tRNA and tmRNA tRNA and tmRNA tRNA prediction tRNA prediction vSNP: add zero coverage vSNP: build tables vSNP: determine reference vSNP: get SNPs vSNP: statistics

AMAS concat AMAS remove AMAS replicate AMAS split AMAS summary Automated multiple sequence Chromeister ClustalW Compalignp DNAdiff Delta-Filter Faffy chunk Faffy extract Faffy merge Format cd-hit outputs Gecko Hammock - cluster peptides Kc-Align MAF Coverage Stats MAFFT MAFFT add MMseqs2 easy-linclust MSABOOT MUSCLE Mummer Mummerplot Nucmer PAL2NAL Paffy add mismatches Paffy chain Paffy dechunk Paffy dedupe Paffy filter Paffy invert Paffy shatter Paffy tile Paffy to bed Paffy trim Paffy upconvert Paffy view SINA Select Sequences Show-Coords cawlign cd-hit chainPreNet chainSort chainSwap hal2fasta hal2maf hal2paf hal2vg halAddToBranch halAlignedExtract halAlignmentDepth halBranchMutations halCoverage halExtract halIndels halLiftover halLodExtract halMaskExtract halPctId halRemoveGenome halRemoveSubtree halRenameGenomes halRenameSequences halReplaceGenome halSnps halStats halSummarizeMutations halSynteny halUpdateBranchLengths halValidate halWiggleLiftover maf2hal mafAddIRows mafCoverage mafFetch mafFrag mafFrags mafGene mashmap netChainSubset netSyntenic trimAl

AEGeAn CanonGFF3 ABySS AEGeAn GAEVAL AEGeAn LocusPocus AEGeAn ParsEval Assemble with MIRA v3.4 Assembly stats BiSCoT Bionano Hybrid Scaffold BlobToolKit CRAQ CRISPR Recognition Tool Cactus Cactus: export Canu assembler Consensus sequence from aligned FASTA Create assemblies with Unicycler DISCO ERGA Assembly Reporting Tool (EAR) Edena (assembling) Edena (overlapping) FBQS Integrator FastK FastK Histex FastK Logex Filter and merge Flye GenomeScope Get annotated regions from genbank files (getorganelle) Get organelle from reads HalfDeep Hapcut2 Hapo-G Hifiasm Hifiasm_meta HyPo IDBA-HYBRID IDBA-TRAN IDBA-UD LINKS Lordec MEGAHIT MITObim Merqury Merqury histogram plot MerquryFK MerquryFK ASMplot MerquryFK CNplot MerquryFK HAPmaker MerquryFK HAPplot Meryl Meryl Meryl Meryl Meryl Meryl Meryl Meryl Minia MitoHiFi NOVOplasty NextDenovo Pairtools Stats Pairtools dedup Pairtools parse Pairtools sort Pairtools split PretextMap Pretextgraph Purge overlaps Quast QuickMerge Racon RagTag Raven Reago RefSeq Masher Contains RefSeq Masher Matches SALSA SOPRA with prebuilt contigs SPAdes SSAKE Shasta Shovill Smudgeplot SyRI TGS-GapCloser Teloscope TrimN Trycycler cluster Trycycler consensus Trycycler partition Trycycler reconcile/msa Trycycler subsample VGP Chromosome Assignment VGP SAK Generation VGP Split AGP VelvetOptimiser WTDBG2 YAHS biosyntheticSPAdes cap3 coronaSPAdes detect CRISPR sequences gfastats instaGRAAL metaSPAdes metaplasmidSPAdes metaviralSPAdes miniasm minipolish necat pilon plasmidSPAdes rnaQUAST rnaSPAdes rnaviralSPAdes velvetg velvetg velveth velveth verkko

Align sequences BBTools: BBMap BWA-MEM2 BWA-MEM2 indexer Bismark Deduplicate Bismark Mapper Bismark Meth. Extractor Bismark Pretty Report Bowtie2 FastGA HISAT2 LASTZ LASTZ_D Lastz paired reads LexicMap Index LexicMap Search Map with BFAST Map with BWA Map with BWA-MEM Map with Bowtie for Illumina Map with Bowtie for SOLiD Map with KMA Map with Mosaik Map with PerM Map with minimap2 Mapper Megablast Owler Parabricks fq2bam Parse blast XML output RNA STAR RNA STARSolo Re-align with SRMA STAR-Fusion TopHat Winnowmap bwameth pbmm2 segemehl wfmash

ARTIC guppyplex ARTIC minion Add LoFreq alignment quality scores Allegro AlphaGenome ISM Scanner AlphaGenome Interval Predictor AlphaGenome Sequence Predictor AlphaGenome Variant Effect AlphaGenome Variant Scorer BBTools: call variants BamLeftAlign Beacon2 Analyses Beacon2 Biosamples Beacon2 Bracket Beacon2 CNV Beacon2 CSV2XLSX Beacon2 Cohorts Beacon2 Datasets Beacon2 Gene Beacon2 Import Beacon2 Individuals Beacon2 PXF2BFF Beacon2 Range Beacon2 Runs Beacon2 Sequence Beacon2 VCF2BFF Beagle CNV Phenopacket CNV VCF2JSON CNVkit Access CNVkit Antitarget CNVkit Autobin CNVkit Batch CNVkit Breaks CNVkit Call CNVkit Coverage CNVkit Diagram CNVkit Export BED CNVkit Export CDT CNVkit Export JTV CNVkit Export Nexus Basics CNVkit Export Nexus OGT CNVkit Export SEG CNVkit Export VCF CNVkit Fix CNVkit Genemetrics CNVkit Heatmap CNVkit Reference CNVkit Scatter CNVkit Segment CNVkit Segmetrics CNVkit Sex CNVkit Target CNVkit Theta Call specific mutations in reads: Call variants Control-FREEC Convert VCF to MAF DCS mutations to SSCS stats: DCS mutations to tags/reads: DeepVariant Delly call Delly classify Delly cnv Delly filter Delly long-read (lr) Delly merge ExomeDepth Extract Variants from gVCF files Finds SNP sites Frameshift Deletions Checks FreeBayes GATK4 ApplyBQSR GATK4 BaseRecalibrator GATK4 HaplotypeCaller GATK4 Mutect2 GATK4 SplitNCigarReads Genehunter-Modscore Get homopolymer run length Insert indel qualities Iris JasmineSV KING LUMPY LUMPY preprocessing Lofreq filter Manta Naive Variant Caller (NVC) Predict variant effects Realign reads SNP distance matrix SnpEff Ensembl CDS SnpEff build: SnpEff chromosome-info: SnpEff databases: SnpEff download: SnpEff eff: SnpEff eff: SnpEff to Peptide fasta SnpSift Annotate SnpSift Annotate SnpSift CaseControl SnpSift CaseControl SnpSift Extract Fields SnpSift Filter SnpSift Filter SnpSift GeneSets SnpSift Intervals SnpSift Intervals SnpSift Variant Type SnpSift dbNSFP SnpSift dbNSFP SnpSift rmInfo SnpSift vcfCheck Strelka Germline Strelka Somatic Swiftlink Tag pileup frequency Tool for Linkage Analysis VCF-BEDintersect: VCF-VCFintersect: VCFaddinfo: VCFannotate: VCFannotateGenotypes: VCFbreakCreateMulti: VCFcheck: VCFcombine: VCFcommonSamples: VCFdistance: VCFfilter: VCFfixup: VCFflatten: VCFgenotype-to-haplotype: VCFgenotypes: VCFhetHomAlleles: VCFleftAlign: VCFprimers: VCFrandomSample: VCFselectsamples: VCFsort: VCFtoTab-delimited: VT normalize VarDict VarScan VarScan copynumber VarScan mpileup VarScan somatic Variant Annotator VcfAllelicPrimitives: basil bcftools List Samples bcftools annotate bcftools call bcftools cnv bcftools color-chrs bcftools concat bcftools consensus bcftools convert from vcf bcftools convert to vcf bcftools counts bcftools csq bcftools dosage bcftools fill-AN-AC bcftools fill-tags bcftools filter bcftools fixploidy bcftools frameshifts bcftools gtcheck bcftools impute-info bcftools isec bcftools mendelian2 bcftools merge bcftools missing2ref bcftools mpileup bcftools norm bcftools query bcftools reheader bcftools roh bcftools setGT bcftools split-vep bcftools stats bcftools tag2tag bcftools view bcftoolsView breseq cuteSV faToVcf fermi2 fermikit-variants hgvsParseR odgi build odgi viz pbgcpp pharmCAT plink sansa annotate seqwish sniffles snippy snippy-clean_full_aln snippy-core som.py and hap.py structureHarvester vcfanno vg convert vg deconstruct vg view

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

blockbuster

Align reads and estimate abundance Alleyoop Annotate DESeq2/DEXSeq output tables Annotate RNAz Arriba Arriba Draw Fusions Arriba Get Filters BAM to Wiggle BAM/SAM Mapping Stats BREW3R.r BlockClust Build expression matrix CEMiTool CIRCexplorer CIRCexplorer2 CMCV CMsearch deoverlap Calculate a Heinz score ChiRA collapse ChiRA extract ChiRA map ChiRA merge ChiRA qauntify Clipping Profile Cofold Compute contig Ex90N50 statistic and Ex90 transcript count Cross-contamination Barcode Filter Cuffcompare Cuffdiff Cufflinks Cuffmerge Cuffnorm Cuffquant DESeq2 DEXSeq DEXSeq-Count Deletion Profile Describe samples Differential expression analysis Dr. Disco (bam-extract) Dr. Disco (classify) Dr. Disco (detect) Dr. Disco (fix) Dr. Disco (integrate) EGSEA Evaluation of RRIs using CheRRI Extract CuffDiff Extract and cluster differentially expressed transcripts FEELnc FPKM Count Filter Combined Transcripts Filter low expression transcripts Fit a BUM model FlaiMapper FuMa GLASSgo Gene Body Coverage (BAM) Gene Body Coverage (Bigwig) Generate SuperTranscripts Generate gene to transcript map GenomicSuperSignature Get RT Stop Counts Get motifs from AREsite2 GraphProt Hexamer frequency IDR Identify optimal scoring subnetwork Infer Experiment Inner Distance Insertion Profile IntaRNA IsoformSwitchAnalyzeR Iterative Mapping Junction Annotation Junction Saturation Kallisto pseudo Kallisto quant Kinfold Kinwalker LocARNA LocARNA Multiple Aligner MEA MiGMAP MiRDeep2 MiRDeep2 Mapper MiRDeep2 Quantifier Mismatch Profile NASTIseq PARalyzer PIPmiR PIPELINE Partition genes into expression clusters PsiCLASS PureCLIP QualiMap Counts QC QualiMap RNA-Seq QC RBPBench RCAS RNA Structure Prediction RNA fragment size RNA2Dfold RNABOB RNALalifold RNALfold RNAPKplex RNASeq samples quality check RNAaliduplex RNAalifold RNAcode RNAcofold RNAcommender RNAdistance RNAduplex RNAeval RNAfold RNAformer RNAheat RNAinverse RNAlien RNApaln RNApdist RNAplex RNAplot RNAshapes RNAsnoop RNAsnp RNAsubopt RNAup RNAz RNAz Cluster RNAz Randomize Aln RNAz Select Seqs RNAz windows RPKM Saturation RSEM calculate expression RSEM prepare reference RSEM trinity fasta to gene map Reactivity Calculation Read Distribution Read Duplication Read GC Read NVC Read Quality Remove Unwanted Variation Sailfish Salmon quant Salmon quantmerge Select Sequences Seurat Seurat Create Seurat Data Management Seurat Find Clusters Seurat Integrate Seurat Preprocessing Seurat Run Dimensional Reduction Seurat Visualize Sfold Slamdunk Sleuth StringTie StringTie merge TEtranscripts TargetFinder Tophat Fusion Post Train a CheRRI model using RRIs TransDecoder Transcript Integrity Number Trinity Trinity Stats Trinotate Visualize antaRNA barrnap blockbuster cmalign cmbuild cmpress cmscan cmsearch cmstat cmv cummeRbund eXpress edgeR featureCounts footprint htseq-count limma maSigPro miRNAture ngsderive strandedness pRESTO AlignSets pRESTO AssemblePairs pRESTO BuildConsensus pRESTO CollapseSeq pRESTO FilterSeq pRESTO MaskPrimers pRESTO PairSeq pRESTO ParseHeaders pRESTO ParseLog pRESTO Partition pRESTOr AbSeq3 Report pizzly plotDEXSeq remuRNA riboWaltz riboWaltz-plot ribotaper part 1: creation of annotation files ribotaper part 2: metagene analysis for P-sites definition ribotaper part 3: ribosome profiling sRNAPipe scPipe segemehl ssHMM tximport

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

CWPair2 Cooler zoomify DREME EpiCSeg - Chromatin segmentation Filter GeneTrack Hicup Deduplicator Hicup Digester Hicup Filter Hicup Mapper Hicup Pipeline Hicup Truncater Hicup to juicer converter Infinium Human Methylation BeadChip MOABS Minfi DMP Minfi DMR Minfi Drop SNPs Minfi Get Beta Minfi Get CN Minfi Get M Minfi Get SNPs Minfi Map to Genome Minfi Mset Minfi Preprocess Funnorm Minfi Preprocess Quantile Minfi QC Minfi Read 450k Minfi Rset MultiGPS RepMatch SEACR cooler csort with tabix cooler_balance cooler_cload_tabix cooler_makebins hifive metilene

Keep or remove selected individuals LDNe estimation Population Genetics Statistics: Split VCF by pop Subsetting SNPs at random from a VCF file VCF filtering

ASTRAL-III Annotate Annotate BLAST parser Convert XMFA to percent identity table DIST2TREE ETE GeneTree splitter ETE lineage generator ETE mod ETE species tree generator ETE taxa DB generator ETE tree viewer FASTA header converter FASTA2DIST Gene Align and Family Aggregator Gene Copy Number Finder GeneSeqToFamily preparation Homology Classifier and Filter HyPhy-B-STILL HyPhy-BGM HyPhy-BUSTED HyPhy-CFEL HyPhy-CLN HyPhy-Conv HyPhy-FADE HyPhy-FEL HyPhy-FUBAR HyPhy-GARD HyPhy-Infer Stasis Clusters HyPhy-MEME HyPhy-PRIME HyPhy-RELAX HyPhy-SLAC HyPhy-SM2019 HyPhy-Summary HyPhy-aBSREL HybPiper List Organisms MrBayes NextAlign Nextclade PACU PACU - mapping PICRUSt2 Add descriptions PICRUSt2 Full pipeline PICRUSt2 Generation of shuffled predictions PICRUSt2 Hidden state prediction (HSP) PICRUSt2 Metagenome prediction PICRUSt2 Pathway abundance inference PICRUSt2 Sequence placement Pangolin PhyML RAxML RAxML-NG Read2Tree Register Account Related Genomes Replace ambiguous codons SNP distance matrix Species tree generator Squirrel Phylo Squirrel QC T-Coffee TreeBeST best TreeBeST best UShER UShER RIPPLES UShER matUtils VCF2DIST VCF2TREE hcluster_sg hcluster_sg parser sarscov2formatter sarscov2summary

BEAM CTD DAVID FunDO GEMMA Analysis GPASS HVIS LD LPS MasterVar to pgSnp PASS Quality control for GWAS analysis Separate pgSnp alleles VCF to pgSnp g:Profiler snpFreq

Alevin Bellavista CITE-seq-Count COSG CSIDE CellTypist Cluster Inspection using RaceID Clustering using RaceID Combine multiple 1D Models Combine multiple 2D Models Construct Expression Set Object DropletUtils DropletUtils Read10x DropletUtils emptyDrops Evaluation Export AnnData Import Anndata InferCNV Initial processing using RaceID Inspect AnnData Inspect Expression Set Object Liana MISTy Liana Multi-Sample Liana Plot Liana Resource Liana Utils Liana methods Lineage Branch Analysis using StemID Lineage computation using StemID Loom operations MCQUANT Manipulate AnnData Manipulate Expression Set Object MuData import and export MuSiC Compare MuSiC Deconvolution RCTD SCEasy Converter Scanpy Inspect and manipulate Scanpy cluster, embed Scanpy filter Scanpy normalize Scanpy plot Scanpy remove confounders Scater: PCA plot Scater: calculate QC metrics Scater: filter SCE Scater: normalize SCE Scater: plot expression frequency Scater: plot library QC Scater: t-SNE plot Selection Sinto barcode Sinto fragments Slice Image SnapATAC2 Clustering SnapATAC2 Metrics SnapATAC2 Plotting SnapATAC2 Preprocessing SnapATAC2 network SnapATAC2 peaks and motif Vizgen VPT - Extract Vizgen VPT - Segment anndata2ri baredSC 1d baredSC 2d drug2cell muon Cluster, analyze, and embed multimodal data muon filter and normalize muon plot scran_normalize velocyto CLI

ASHLAR BaSiC Illumination MCQUANT Perform segmentation of multiplexed tissue data SpatialData IO SpatialData Operations SpatialData Plot UNetCoreograph UnMicst s3segmenter

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

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

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

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

BBTools: call variants BLAST Reciprocal Best Hits (RBH) BLAST XML to tabular BLAST top hit descriptions Diamond Diamond makedb Diamond view Embed Query Sequences Magic-BLAST: map large RNA or DNA sequences NCBI BLAST+ blastdbcmd entry(s) NCBI BLAST+ blastn NCBI BLAST+ blastp NCBI BLAST+ blastx NCBI BLAST+ convert2blastmask NCBI BLAST+ database info NCBI BLAST+ dustmasker NCBI BLAST+ makeblastdb NCBI BLAST+ makeprofiledb NCBI BLAST+ rpsblast NCBI BLAST+ rpstblastn NCBI BLAST+ segmasker NCBI BLAST+ tblastn NCBI BLAST+ tblastx NCBI get species taxids Search Protein Database Search Protein Database

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

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

Stanford CoreNLP Annotators (Multi-language) spaCy NLP Annotators

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

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

ALDEx2 ANCOM-BC Add Rank Names to Phyloseq Object Barplot BiG-SCAPE Binette Binning refiner Biobox add taxid Bracken CAMI AMBER CAMI AMBER add length column CAMI AMBER convert to biobox CAT add_names CAT bins CAT contigs CAT prepare CAT summarise COMEBin CONCOCT CONCOCT: Cut up contigs CONCOCT: Extract a fasta file CONCOCT: Generate the input coverage table CONCOCT: Merge cut clusters Calculate KEGG Pathways completeness Calculate contig depths CheckM analyze CheckM lineage_set CheckM lineage_wf CheckM plot CheckM qa CheckM taxon_set CheckM taxonomy_wf CheckM tetra CheckM tree CheckM tree_qa Chimera.vsearch Combine MetaPhlAn and HUMAnN outputs Compare BIOM tables Convert Kraken Converts genome bins in fasta format CoverM contig CoverM genome Create phyloseq object Create phyloseq object Customize the marker sequences and metadata DAS Tool DRAM annotate DRAM distill DRAM find neighborhoods DRAM merge multiple annotations DRAM strain annotations Decontam DefenseFinder EukRep Extract the marker sequences and metadata Fairy coverage Fairy sketch FastSpar: Reduce correlation table FastSpar: estimate p-values Filter RefSeq by taxonomy Format MetaPhlAn2 Format MetaPhlAn2 Fur GAMMA GAMMA-S GDCWebApp GTDB-Tk Classify genomes Generate BAM file for COMEBin Generate heatmap Generation, personalization and annotation of tree HAllA HUMAnN ITSx InStrain Compare InStrain Profile Join (merge) Kleborate Kmer2Stats KneadData Kraken Kraken taxonomic report Kraken-biom Kraken-filter Kraken-mpa-report Kraken-report Kraken-translate Kraken2 Krakentools: Calculates alpha diversity Krakentools: Combine multiple Kraken reports Krakentools: Convert kraken report file Krakentools: Convert kraken report file Krakentools: Extract Kraken Reads By ID Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) Krona pie chart LAST-split LAST-train LASTal LASTdb LotuS2 MAF-convert MALT analyzer MAPseq MEGAN Blast2LCA: apply LCA alignment MEGAN: Extract reads MEGAN: Generate RMA files MEGAN: Generate a MEGAN rma6 file MEGAN: Generate a MEGAN rma6 file MEGAN: Get information MEGAN: meganize a DIAMOND file MGnify genome search MGnify: Classify rRNA variable regions MGnify: Generate ASV abundance and Krona tables MGnify: Generate Reverse Complements of reverse Primers MGnify: MAPseq to ASV taxonomy table MGnify: Permute primers MGnify: Primer Validation and Classification MT2MQ MaAsLin 2 MaAsLin3 Map SNV MaxBin2 Merge Merge MetaBAT2 MetaEuk Easy Predict MetaGeneAnnotator MetaPhlAn MetaWRAP MetaWRAP Metagenomics toolkit Bulk Download Metagenomics toolkit Original Metadata NCBI-GTDB map Name2taxid Nonpareil Normalize PHI toolkit report PIMENTO Are there primers? PIMENTO Choose primer cutoff PIMENTO Find cutoffs PIMENTO Generate base-conservation vector(s) PIMENTO Primer cutoff prediction PIMENTO Standard primer matching Phyloseq Taxonomic Agglomeration Phyloseq: Bar Chart Phyloseq: plot alpha diverstiy measure Phyloseq: plot ordination PlasFlow Polypolish Profile2CAMI Recentrifuge Reduce Regroup Rename features Renormalize SIRIUS-CSI:FingerID SRST2 Salmonella Subtyping SameStr Compare SameStr Convert SameStr Extract SameStr Filter SameStr Merge SameStr Stats SameStr Summarize Scoary SemiBin SemiBin: Concatenate fasta files SemiBin: Contig annotations SemiBin: Generate sequence features SemiBin: Group the contigs SemiBin: Train SeqSero2 Split Split a HUMAnN table Unpack pathway abundances VALET VAPOR VIBRANT VSearch alignment VSearch chimera detection VSearch clustering VSearch dereplication VSearch masking VSearch search VSearch shuffling VSearch sorting Vegan Diversity Vegan Fisher Alpha Vegan Rarefaction VirSorter ampvis2 OTU network plot ampvis2 alpha diversity ampvis2 boxplot ampvis2 core community analysis ampvis2 export fasta ampvis2 export otu ampvis2 frequency plot ampvis2 heatmap ampvis2 load ampvis2 merge ampvis2 data sets ampvis2 merge replicates ampvis2 octave plot ampvis2 ordination plot ampvis2 rank abundance plot ampvis2 rarefaction curve ampvis2 set metadata ampvis2 subset data ampvis2 subset samples ampvis2 timeseries plot ampvis2 venn diagram bmtagger checkm2 dRep compare dRep dereplicate dada2: assignTaxonomy and addSpecies dada2: dada dada2: filterAndTrim dada2: learnErrors dada2: makeSequenceTable dada2: mergePairs dada2: plotComplexity dada2: plotQualityProfile dada2: primer check dada2: removeBimeraDenovo dada2: sequence counts geNomad iPHoP predict index jellyfish kMetaShot kaiju kaiju-addTaxonNames kaiju-mergeOutputs kaiju2krona kaiju2table khmer: Abundance Distribution khmer: Abundance Distribution (all-in-one) khmer: Count Median khmer: Extract partitions khmer: Filter reads khmer: Filter reads khmer: Normalize By Median khmer: Sequence partition all-in-one kmindex build kmindex query mOTUs_profiler mash dist mash paste mash screen mash sketch metaMDBG assemble (ASM) metaMDBG graph (GFA) metabuli classify metagenomeSeq Normalization micro_decon mmuphin profile qiime2 dada2 denoise-ccs qiime2 dbOTU sixgill build sixgill filter sixgill makefasta sixgill merge staramr sylph profile sylph query taxpasta tiara vConTACT2 vConTACT2 gene2genome vRhyme virAnnot Blast2tsv virAnnot OTU virAnnot Rps2tsv xcms findChromPeaks (xcmsSet)

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

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

Illuminapairedend NGSfilter obiannotate obiclean obiconvert obigrep obimultiplex obipairing obisort obistat obitab obiuniq

Cojac: mutbamscan Cojac: pubmut Cojac: tabmut Freyja: Aggregate and visualize Freyja: Bootstrapping Freyja: Call variants Freyja: Demix IRMA Make inferences Read It and Keep VIRULIGN Variant Frequency Plot VirHEAT: visualize allele frequencies ivar consensus ivar filtervariants ivar getmasked ivar removereads ivar trim ivar variants lineagespot snipit varVAMP viralverify

AccurateMassSearch AdditiveSeries AssayGeneratorMetabo BaselineFilter CVInspector Calculate protein properties ClusterMassTraces ClusterMassTracesByPrecursor Colabfold Alphafold Colabfold MSA CometAdapter CompNovo CompNovoCID ConsensusID ConsensusMapNormalizer Constava ConvertFastaToPrositCSV ConvertLibraryToBlib ConvertPrositCSVToLibrary Create Decoy Database (reverse) Create nested list CruxAdapter CustomProDB DIA-NN DIA_Umpire_SE DIAlignR DTAExtractor DatabaseFilter DeMeanderize Decharger DecoyDatabase Diffacto Digestor DigestorMotif EICExtractor ERPairFinder EncyclopeDIA EncyclopeDIA Quantify Epifany ExternalCalibration FASTG2Protlib-Peptides FASTG2Protlib-Validate FFEval FalseDiscoveryRate FastaCLI FeatureFinderCentroided FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMRM FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMultiplex FeatureFinderSuperHirn FeatureLinkerLabeled FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FidoAdapter FileConverter FileFilter FileInfo FileMerger FlashLFQ FragPipe - Academic Research and Education User License (Non-Commercial) FragPipe Manifest Generator FuzzyDiff GNPSExport Hardklor HighResPrecursorMassCorrector IDConflictResolver IDDecoyProbability IDExtractor IDFileConverter IDFilter IDMapper IDMassAccuracy IDMerger IDPosteriorErrorProbability IDRTCalibration IDRipper IDScoreSwitcher IDSplitter Identification Parameters InclusionExclusionListCreator InspectAdapter InternalCalibration IsobaricAnalyzer JSONExporter Kronik Label free protein LabeledEval LowMemPeakPickerHiRes LowMemPeakPickerHiResRandomAccess LowMemPeakPickerHiResRandomAccess LuciphorAdapter MALDIquant peak detection MALDIquant preprocessing MRMMapper MRMPairFinder MRMTransitionGroupPicker MS-GF+ MSFraggerAdapter MSGFPlusAdapter MSI Qualitycontrol MSI classification MSI colocalization MSI combine MSI data exporter MSI filtering MSI group comparison MSI mz images MSI plot spectra MSI preprocessing MSI segmentation MSI single ion segmentation MSSimulator MSstats MSstatsConverter MSstatsTMT MT2MQ MaRaClusterAdapter MapAlignerIdentification MapAlignerPoseClustering MapAlignerSpectrum MapAlignerTreeGuided MapNormalizer MapRTTransformer MapStatistics MascotAdapter MascotAdapterOnline MassCalculator MassTraceExtractor MaxQuant MaxQuant (using mqpar.xml) MaxQuant Phosphopeptide ANOVA MaxQuant Phosphopeptide Preprocessing MetaNovo MetaProSIP MetaProteomeAnalyzer MetaboliteAdductDecharger MetaboliteSpectralMatcher Morpheus MultiplexResolver MyriMatch MyriMatchAdapter MzMLSplitter MzTabExporter NetMHCPan NetMHCiiPan NoiseFilterGaussian NoiseFilterSGolay NovorAdapter NucleicAcidSearchEngine OMSSAAdapter OpenMSInfo OpenPepXL OpenPepXLLF OpenSwathAnalyzer OpenSwathAssayGenerator OpenSwathChromatogramExtractor OpenSwathConfidenceScoring OpenSwathDIAPreScoring OpenSwathDecoyGenerator OpenSwathFeatureXMLToTSV OpenSwathFileSplitter OpenSwathMzMLFileCacher OpenSwathRTNormalizer OpenSwathRewriteToFeatureXML OpenSwathWorkflow PSM-Fragment Validator PSMFeatureExtractor PTModel PTPredict Pathway Matcher PeakPickerHiRes PeakPickerIterative PeakPickerWavelet PepNovoAdapter PepPointer PepQuery PepQuery2 PepQuery2 Show Sets PepQuery2 index Peptide Genomic Coordinate Peptide Shaker PeptideIndexer Percolator PercolatorAdapter PhosphoScoring Pout2mzid PrecursorIonSelector PrecursorMassCorrector Protease prediction Protease prediction ProteinInference ProteinQuantifier ProteinResolver Proteinortho Proteinortho clustering Proteinortho grab proteins Proteinortho summary ProteomIQon MzMLToMzLite ProteomIQon PSMStatistics ProteomIQon PeptideDB ProteomIQon PeptideSpectrumMatching ProteomIQon ProteinInference Proteomiqon JoinQuantPepIonsWithProteins Proteomiqon LabelFreeProteinQuantification Proteomiqon LabeledProteinQuantification Proteomiqon PSMBasedQuantification PyProphet export PyProphet merge PyProphet peptide PyProphet protein PyProphet score PyProphet subsample QCCalculator QCEmbedder QCExporter QCExtractor QCImporter QCMerger QCShrinker QuPath ROI Splitter QualityControl QuanTP QuantWiz-IQ RNADigestor RNAMassCalculator RNPxl RNPxlSearch RNPxlXICFilter RTEvaluation RTModel RTPredict Raw Tools Remove protonation state SWISS-MODEL Modelling API SageAdapter Scop3P Search GUI Search engine output to Pin converter SearchToLib SeedListGenerator SemanticValidator SequenceCoverageCalculator SimpleSearchEngine SiriusAdapter SpecLibCreator SpecLibSearcher SpectraFilterBernNorm SpectraFilterMarkerMower SpectraFilterNLargest SpectraFilterNormalizer SpectraFilterParentPeakMower SpectraFilterScaler SpectraFilterSqrtMower SpectraFilterThresholdMower SpectraFilterWindowMower SpectraMerger SpectraSTSearchAdapter SvmTheoreticalSpectrumGeneratorTrainer TICCalculator TOFCalibration TRIC TargetedFileConverter TextExporter TopPerc TransformationEvaluation Unipept Validate FASTA Database Walnut X!Tandem MSMS Search X!Tandem MSMS Search XFDR XMLValidator XTandemAdapter Zeiss laser-capture microdissection converter bioconductor-scp calisp diapysef library generation eggNOG Mapper eggNOG Mapper eggNOG Mapper idpAssemble idpEmbedder idpQonvert idpQuery megahit contig2fastg metaQuantome: create samples file metaQuantome: database metaQuantome: expand metaQuantome: filter metaQuantome: stat metaQuantome: visualize moFF pVACbind prot-scriber pyteomics syndiva

ASCA Align Samples Anova Batch_correction Between-table Correlation BioTransformer Biosigner Blank Filter CAMERA.annotate CAMERA.combinexsAnnos Calculate flux distribution Check Format Convert DIMSpy-based HDF5 to tsv Determine_batch_correction Flux variability analysis (FVA) GC derivatization Gene knockout analysis Generic_Filter Get exchange bounds Get peaklists Golm Metabolome Database search spectrum HMDB MS search Heatmap ID choice Intensity Check Isoplot: Generate plots from isocor output Join +/- Ions LCMS matching Lipidmaps MFAssignR FindRecalSeries MFAssignR HistNoise MFAssignR IsoFiltR MFAssignR KMDNoise MFAssignR MFAssign MFAssignR MFAssignCHO MFAssignR Recal MFAssignR RecalList MFAssignR SNplot MS Target Screening MS2DeepScore Configuration Generator MS2DeepScore Model Training MS2DeepScore Similarity MSMetaEnhancer MSnbase readMSData MZMine batch Make GEM quality report MassBank spectrum searches Merge peaklists MetFrag MetFrag Vis Missing Values Sample Filter Multilevel Multivariate NMR spectra alignment NMR_Annotation NMR_Bucketing NMR_Normalization NMR_Preprocessing NMR_Read Normalization OPLS-DA_Contrasts Pathway visualization Phenotype phase plane (PhPP) ProbMetab Tool Process Scans (and SIM-Stitch) Quality Metrics RAMClustR RAMClustR define experiment RECETOX MsFinder RIAssigner RIAssigner init from comment RMassBank Rename Annotated Feature Replicate Filter SIRIUS-CSI:FingerID Sample Filter Skyline2Isocor: converting skyling outputs into IsoCor inputs Table Merge Transformation Univariate W4m Data Subset WaveICA bank_inhouse bioconductor-msnbase centroid bioconductor-msnbase smooth chromatogram bioconductor-msnbase smooth mz dimet abundance plot dimet bivariate analysis dimet differential analysis dimet differential multigroup analysis dimet enrichment plot dimet isotopologues plot dimet metabologram dimet pca analysis dimet pca plot dimet timecourse analysis genform isolib matchms add key matchms convert matchms filtering matchms fingerprint similarity matchms metadata export matchms metadata match matchms metadata merge matchms networking matchms remove key matchms remove spectra matchms scores formatter matchms similarity matchms spectral similarity matchms split library matchms subsetting metaMS.runGC mixmodel mixmodel msPurity.averageFragSpectra msPurity.createDatabase msPurity.createMSP msPurity.dimsPredictPuritySingle msPurity.filterFragSpectra msPurity.flagRemove msPurity.frag4feature msPurity.purityA msPurity.purityX msPurity.spectralMatching proFIA rcx-tk recetox-aplcms - align features recetox-aplcms - compute clusters recetox-aplcms - compute template recetox-aplcms - correct time recetox-aplcms - generate feature table recetox-aplcms - merge known table recetox-aplcms - recover weaker signals recetox-aplcms - remove noise recetox-xMSannotator spec2vec model training spec2vec similarity table arithmetics table column transformations table rename column table rename columns via regex table scipy interpolate tracegroomer use theoretical m/z values xcms adjustRtime (retcor) xcms fillChromPeaks (fillPeaks) xcms findChromPeaks (xcmsSet) xcms findChromPeaks Merger xcms get a sampleMetadata file xcms groupChromPeaks (group) xcms plot chromatogram xcms plot eic xcms plot raw xcms process history xcms refineChromPeaks (refine)

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

Canonical Correlation Analysis Correlation Count Count GFF Features Create a model to recommend tools Distance matrix-based hierarchical clustering Draw ROC plot FastSpar Generate A Matrix GraphEmbed IPFP Normalisation IWTomics Load IWTomics Plot with Threshold IWTomics Test Kernel Canonical Correlation Analysis Kernel Principal Component Analysis MINE Nearest Neighbors Classification Perform Best-subsets Regression Perform LDA Plot actual vs predicted curves and residual plots Plot confusion matrix, precision, recall and ROC and AUC curves Principal Component Analysis RGCCA Rolling window SaQC Sequence composition Sparse Matrix Functions Statistical hypothesis testing Summary Statistics T Test for Two Samples Wavelet variance

Build Deep learning Batch Training Models Calculate metrics Calculate metrics Cleanlab Issue Handler Create a deep learning model architecture Create a model to recommend tools Create deep learning model Deep learning training and evaluation DeepMicro Discriminant Analysis Ensemble methods Estimator attributes Evaluate a Fitted Model Evaluate pairwise distances FLUX Feature Selection Fit a Pipeline, Ensemble Flexynesis Flexynesis Inference Flexynesis cBioPortal import Flexynesis plot Flexynesis utils Generalized linear models Generate Hyperparameter Search LLM Hub Label encoder LightGBM MCL Machine Learning Visualization Extension Model Prediction Model Validation Nearest Neighbors Classification Numeric Clustering Pipeline Builder Prediction of Breast Cancer (BC) Preprocess Principal component analysis RAG Retriever Random Forest model Sparse Matrix Functions Speech to Text Speech to Text with Diarization Split Dataset Stacking Ensembles Support vector machines (SVMs) Tabular data prediction using TabPFN To categorical Train, Test and Evaluation aoptk chemical identifier aoptk publication tracker chatGPT chopin2 decontaminator virhunter

DeepForestVision SAM3 Semantic Segmentation

BAM Coverage Plotter Bandage Image Bandage Info Bar chart Barplot w ggplot2 Boxplot Boxplot w ggplot2 Build custom track Calculate Contrast threshold Circos Circos: Alignments to links Circos: Bundle Links Circos: Interval to Circos Text Labels Circos: Interval to Tiles Circos: Link Density Track Circos: Resample 1/2D data Circos: Stack bigWigs as Histogram Circos: Table viewer Circos: bigWig to Scatter Export to GraPhlAn Fasta nucleotide color plot Fasta nucleotide color plot GC Skew GMAJ Generate a word cloud Generation, personalization and annotation of tree GraPhlAn Heatmap w ggplot Histogram Histogram with ggplot2 JBrowse JBrowse - Data Directory to Standalone JBrowse2 Karyotype Plotting tool Linear Genome Plot MA plot MUMmer dotplot Manhattan Plots Manhattan plot Newick Display PCA plot w ggplot2 Paired-end histogram Pairwise intersection Parallel Coordinates Plot Pathifier Pathview Plot actual vs predicted curves and residual plots Plot confusion matrix, precision, recall and ROC and AUC curves Plotting tool Pretext Snapshot Scatterplot Scatterplot with ggplot2 SimpleWeather UpSet diagram VCF to MAF Custom Track Venn Diagram Violin plot w ggplot2 Visualize with Krona Volcano Plot gene.iobio visualisation ggupset heatmap2 pyGenomeTracks rtsne seaborn seaborn pair-wise scatterplot upset plot

MuDirac MuSpinSim Combine MuSpinSim Configure MuSpinSim Plot MuSpinSim Simulate PyMuonSuite AIRSS Cluster PyMuonSuite AIRSS UEP Optimise PyMuonSuite Phonons PyMuonSuite Symmetry cif2cell

Larch Artemis Larch Athena Larch Criteria Report Larch FEFF Larch LCF Larch Plot Larch Select Paths

BRT tool prediction Clara Estimate and Clustering ClaraClust ClusterEstimate EcoMap GeoNearestNeighbor Indicspecies TaxaSeeker

CRSconverter EstimEndem PhylOccuMatcher PhyloIndex

Bar plot DIVAnd Geometric means Make a map with a shapefile

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

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

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

Diversity IVR QECB-Dissimilarity

3DTrees: LAS/LAZ Standardization 3DTrees: SmartTile 3Dtrees: DetailView 3Dtrees: Overviews 3Dtrees: Potree Converter 3Dtrees: Py3DTiles Converter 3Dtrees: RayCloudTools 3Dtrees: SegmentAnyTree 3Dtrees: Tile and Merge AquaINFRA OGC API Processes Copernicus CDS Downloader for AquaINFRA marine model Copernicus CMEMS Downloader for AquaINFRA marine model GDAL Build VRT GDAL Informations GDAL Merge GDAL Translate GDAL Warp GDAL addo Hirondelle CRIM OGC API Processes NetCDF xarray Coordinate Info NetCDF xarray Metadata Info NetCDF xarray Selection NetCDF xarray map plotting NetCDF xarray operations OGR Informations OGR2ogr OTB.BandMath OTB.MeanShiftSmoothing Run interpolation Terrabyte OGC API Processes Zoo Project OGC API Processes

BioGeoChemical calibration CDO Operations CDO get info CESM CTSM/FATES-EMERALD Canyon-B Copernicus Atmosphere Data Store Copernicus Climate Data Store Copernicus Essential Climate Variables EODIE Land cover degradation NetCDF timeseries Extractor ODV collection manager ODV history manager QCV harmonizer climate stripes map plot shift longitudes zonal statistics

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

EML to EAL Eml validate: Make EML Make annotations template Make data paper sketches Make entities templates for raster, vector and other entities files Make geographic coverage template Make taxonomic coverage template Make templates Make templates for data tables Make templates for raster files Make templates for vector files

CREx Compute distance matrix IQ-TREE Join neighbors Merge matching reads Mutate Codons Quicktree Structure TN93 TN93 Cluster TN93 Filter codeML mapDamage

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

Base Count Calculate protein properties ChIPpeakAnno annoPeaks Cluster Profiler Bitr Cluster Profiler GO Codon count Concatenate Icenet Data Extract sequences from GenBank GFF converter GenBank and EBML Icenet Forecast InterProphet MFA Adapt MFA Align MFA Find OOVs MFA G2P MFA Remap Alignments MFA Tokenize MFA Train MFA Train Dictionary MFA Train G2P MFA Train LM MFA Train Tokenizer MFA Validate MFA Validate Dictionary MLST, AMRfinder, and STARamr Analysis NetCDF to Zarr Peptide Prophet Personal Cancer Genome Reporter Preprocess Icenet Data Protein Prophet PyIron QUAST Analysis and FASTA Generator Quality Control FastP Bracken RNALfoldz Sequence converter Tombo Re-squiggle Tombo create Tombo detect modifications Tombo plot genome locations Tombo plot most signficant Translate nucleotides Visualize Icenet Forecast Vowel formant extraction bwtool-lift create API requests for Icenet Data zeppelin

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

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

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

Adapt an elastic transformation Add or remove noise Add shadow effect Adjust threshold Align two images Analyze and visualize spatial multi-omics data Analyze particles Analyze skeleton Apply a morphological operation Apply anisotropic diffusion Apply elastic transformation Apply raw transformation Apply ridge filter Apply standard image filter Build a workflow with BiaPy COCO to LabelMe JSON Converter Clip image intensities Colocalization ColorToGray Colorize label map Compare elastic and raw deformation Compare opposite elastic deformations Compare two raw deformations Compose a raw and an elastic transformation Compose two elastic transformations Compose two raw transformations Compute Voronoi tessellation Compute image features Compute image orientation Compute image segmentation and object detection performance measures Concatenate images Convert Anndata to CSV Convert AnyLabeling JSON to YOLO text Convert DICOM to TIFF Convert binary image to EDM Convert binary image to label map Convert binary image to points (center of masses) Convert binary image to points (point coordinates) Convert coordinates to label map Convert elastic transformation to raw Convert image format Convert label map to binary image Convert label map to points (center of masses) Convert single-channel to multi-channel image Convert to OME-Zarr Convert to binary ConvertObjectsToImage Count objects in label map Create new image Create spatial scatterplot Crop image DisplayDataOnImage DocLayout-YOLO Download IDR/OMERO Enhance contrast EnhanceOrSuppressFeatures Evaluate segmentation Export DICOM metadata ExportToSpreadsheet Extract image features Extract top view from whole-slide image Extract video frames FTP Link for Bioimage Archive Filter label map by rules Find datasets with similar ISCC-CODEs Find edges Find maxima Generate ISCC-CODE GrayToColor IdentifyPrimaryObjects Image Converter Image Montage ImageMath MaskImage MeasureGranularity MeasureImageAreaOccupied MeasureImageIntensity MeasureImageQuality MeasureObjectIntensity MeasureObjectSizeShape MeasureTexture Merge neighbors in label map OMERO Dataset to Plate OMERO IDs OMERO Image Import OMERO Metadata Import OMERO ROI Import OMERO get IDs OMERO get Object Operate on pixels Overlay Overlay Segmentation Mask Overlay images OverlayOutlines Page dewarp Perform 2-D spot detection Perform YOLO image labeling Perform YOLO training Perform affine image registration (intensity-based) Perform affine image registration (landmark-based) Perform color deconvolution or transformation Perform curve fitting Perform gating Perform histogram equalization Perform linking in time series (nearest neighbors) Perform segmentation in densely packed 3-D volumetric images Perform segmentation using deformable shape models Perform segmentation using region-based fitting of overlapping ellipses Perform segmentation using watershed transformation Perform wavelet transformation on 3D-image stack Performs projective transformation Performs projective transformation with/without labels Permutate image axes Process image using a BioImage.IO model Process images using arithmetic expressions Process single-cell intensities RelateObjects Remove image background Rename OME-TIFF channels Render 3-D image data Run CellProfiler pipeline Run CellProfiler pipeline Run generalist cell and nucleus segmentation Run generalist cell and nucleus segmentation SaveImages Scale image Sharpen Show image info Skeletonize Slice image into patches Smooth image Split image along axes Split label map using morphological operators Starting Modules Switch axis coordinates Tesseract Threshold image Tile TrackObjects Verify ISCC-CODE Visualize detections Vitessce Wound healing scratch assay jdeskew pdfimages

Astronomical Archives (IVOA) CRbeam CTA DESI Legacy Survey GRB detection GWTC HESS Plot Tools SGWB analyse-short-astro-text astropy fits2bitmap astropy fits2csv astropy fitsinfo csv2fits fits2tiff source-extractor

AnyLabeling Interactive AskOmics BellaVista Interactive COPASI Cell Journey CellPose Interactive Copernicus Data Space Ecosystem Dot EtherCalc GPU-enabled Interactive Jupyter Notebook for Machine Learning GeneNoteBook HiGlass Holoviz IDEAL Ilastik Interactive BlobToolKit Interactive CELLxGENE Environment Interactive CELLxGENE VIP Environment Interactive Climate Notebook Interactive DIVAnd Notebooks Interactive Hdfview tool Interactive JupyterGIS Notebook Interactive JupyterLab Notebook Interactive MGnify Notebook Interactive Mouse Sciatic Nerve CellxGene Environment Interactive Pangeo Machine Learning Notebook Interactive Pangeo Notebook Interactive Source Notebooks LiberTEM NEAL Neo4j (Graph Database) ODV OpenRefine Panoply Paraview Pavian Phinch Visualisation Phyloseq PhysiCell Studio PretextView PyIron Interactive Jupyter Notebook QGIS Qiskit Jupyter notebook QuPath RStudio RStudio AskoR Run CellProfiler Run Napari STAC catalog Scoop3-Argo SimText Terriamap VCF (iobio) Visualisation VRM Editor Wallace Wilson bam.iobio visualisation geoexplorer iSEE metashark metashrimps pampa radiant tadviewer

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

EBI SCXA Data Retrieval GTF2GeneList Human Cell Atlas Matrix Downloader UCSC Cell Browser

BasicDesign CarveMe DBKit Create DBKit Extract DBKit Merge DNA-Bot FSD Before/After: FSD regions: FSD: Flux balance analysis Get PubMed abstracts IRIS-TCGA Ligase Chain Reaction Genie Load packaged annotation data NCBI ECitMatch NCBI EFetch NCBI EFetch NCBI EInfo NCBI EInfo NCBI ELink NCBI EPost NCBI ESearch NCBI ESearch NCBI ESummary Optimal Design of Experiment PMIDs to PubTator PubMed query RP2paths RRules Parser SPRING Cross SPRING MCC SPRING Map SPRING Min-Z SPRING Model SPRING Model-All SbmlToSbol Selenzyme StrainDesign analyzing-model StrainDesign reduce-model StrainDesign simulate-deletion TD: Text to wordmatrix pcdl_get_anndata pcdl_get_cell_attribute pcdl_get_cell_attribute_list pcdl_get_cell_df pcdl_get_celltype_list pcdl_get_conc_attribute pcdl_get_conc_df pcdl_get_substrate_list pcdl_get_unit_dict pcdl_get_version pcdl_make_cell_vtk pcdl_make_conc_vtk pcdl_make_gif pcdl_make_graph_gml pcdl_make_movie pcdl_plot_contour pcdl_plot_scatter pcdl_plot_timeseries rp2biosensor

tracy Align tracy Assemble tracy Basecall tracy Decompose

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

QIIME vizualisation extractor qiime2 alignment mafft qiime2 alignment mafft-add qiime2 alignment mask qiime2 composition add-pseudocount qiime2 composition ancom qiime2 composition ancombc qiime2 composition tabulate qiime2 cutadapt demux-paired qiime2 cutadapt demux-single qiime2 cutadapt trim-paired qiime2 cutadapt trim-single qiime2 dada2 denoise-ccs qiime2 dada2 denoise-paired qiime2 dada2 denoise-pyro qiime2 dada2 denoise-single qiime2 deblur denoise-16S qiime2 deblur denoise-other qiime2 deblur visualize-stats qiime2 demux emp-paired qiime2 demux emp-single qiime2 demux filter-samples qiime2 demux subsample-paired qiime2 demux subsample-single qiime2 demux summarize qiime2 diversity adonis qiime2 diversity alpha qiime2 diversity alpha-correlation qiime2 diversity alpha-group-significance qiime2 diversity alpha-phylogenetic qiime2 diversity alpha-rarefaction qiime2 diversity beta qiime2 diversity beta-correlation qiime2 diversity beta-group-significance qiime2 diversity beta-phylogenetic qiime2 diversity beta-rarefaction qiime2 diversity bioenv qiime2 diversity core-metrics qiime2 diversity core-metrics-phylogenetic qiime2 diversity filter-alpha-diversity qiime2 diversity filter-distance-matrix qiime2 diversity mantel qiime2 diversity pcoa qiime2 diversity pcoa-biplot qiime2 diversity procrustes-analysis qiime2 diversity tsne qiime2 diversity umap qiime2 diversity-lib alpha-passthrough qiime2 diversity-lib beta-passthrough qiime2 diversity-lib beta-phylogenetic-meta-passthrough qiime2 diversity-lib beta-phylogenetic-passthrough qiime2 diversity-lib bray-curtis qiime2 diversity-lib faith-pd qiime2 diversity-lib jaccard qiime2 diversity-lib observed-features qiime2 diversity-lib pielou-evenness qiime2 diversity-lib shannon-entropy qiime2 diversity-lib unweighted-unifrac qiime2 diversity-lib weighted-unifrac qiime2 emperor biplot qiime2 emperor plot qiime2 emperor procrustes-plot qiime2 feature-classifier blast qiime2 feature-classifier classify-consensus-blast qiime2 feature-classifier classify-consensus-vsearch qiime2 feature-classifier classify-hybrid-vsearch-sklearn qiime2 feature-classifier classify-sklearn qiime2 feature-classifier extract-reads qiime2 feature-classifier find-consensus-annotation qiime2 feature-classifier fit-classifier-naive-bayes qiime2 feature-classifier fit-classifier-sklearn qiime2 feature-classifier vsearch-global qiime2 feature-table core-features qiime2 feature-table filter-features qiime2 feature-table filter-features-conditionally qiime2 feature-table filter-samples qiime2 feature-table filter-seqs qiime2 feature-table group qiime2 feature-table heatmap qiime2 feature-table merge qiime2 feature-table merge-seqs qiime2 feature-table merge-taxa qiime2 feature-table presence-absence qiime2 feature-table rarefy qiime2 feature-table relative-frequency qiime2 feature-table rename-ids qiime2 feature-table subsample qiime2 feature-table summarize qiime2 feature-table tabulate-seqs qiime2 feature-table transpose qiime2 fragment-insertion classify-otus-experimental qiime2 fragment-insertion filter-features qiime2 fragment-insertion sepp qiime2 gneiss assign-ids qiime2 gneiss correlation-clustering qiime2 gneiss dendrogram-heatmap qiime2 gneiss gradient-clustering qiime2 gneiss ilr-hierarchical qiime2 gneiss ilr-phylogenetic qiime2 gneiss ilr-phylogenetic-differential qiime2 gneiss ilr-phylogenetic-ordination qiime2 longitudinal anova qiime2 longitudinal feature-volatility qiime2 longitudinal first-differences qiime2 longitudinal first-distances qiime2 longitudinal linear-mixed-effects qiime2 longitudinal maturity-index qiime2 longitudinal nmit qiime2 longitudinal pairwise-differences qiime2 longitudinal pairwise-distances qiime2 longitudinal plot-feature-volatility qiime2 longitudinal volatility qiime2 metadata distance-matrix qiime2 metadata shuffle-groups qiime2 metadata tabulate qiime2 phylogeny align-to-tree-mafft-fasttree qiime2 phylogeny align-to-tree-mafft-iqtree qiime2 phylogeny align-to-tree-mafft-raxml qiime2 phylogeny fasttree qiime2 phylogeny filter-table 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 quality-control bowtie2-build qiime2 quality-control evaluate-composition qiime2 quality-control evaluate-seqs qiime2 quality-control evaluate-taxonomy qiime2 quality-control exclude-seqs qiime2 quality-control filter-reads qiime2 quality-filter q-score qiime2 rescript get-bv-brc-genome-features qiime2 rescript get-bv-brc-genomes qiime2 rescript get-bv-brc-metadata qiime2 sample-classifier classify-samples qiime2 sample-classifier classify-samples-from-dist qiime2 sample-classifier classify-samples-ncv qiime2 sample-classifier confusion-matrix qiime2 sample-classifier fit-classifier qiime2 sample-classifier fit-regressor qiime2 sample-classifier heatmap qiime2 sample-classifier metatable qiime2 sample-classifier predict-classification qiime2 sample-classifier predict-regression qiime2 sample-classifier regress-samples qiime2 sample-classifier regress-samples-ncv qiime2 sample-classifier scatterplot qiime2 sample-classifier split-table qiime2 sample-classifier summarize qiime2 stats alpha-group-significance qiime2 stats collate-stats qiime2 stats facet-across qiime2 stats facet-within qiime2 stats mann-whitney-u-facet qiime2 stats plot-rainclouds qiime2 stats prep-alpha-distribution qiime2 stats wilcoxon-srt qiime2 stats wilcoxon-srt-facet qiime2 taxa barplot qiime2 taxa collapse qiime2 taxa filter-seqs qiime2 taxa filter-table qiime2 tools export qiime2 tools import qiime2 tools import-fastq qiime2 vizard boxplot qiime2 vizard heatmap qiime2 vizard lineplot qiime2 vizard scatterplot-2d qiime2 vsearch cluster-features-closed-reference qiime2 vsearch cluster-features-de-novo qiime2 vsearch cluster-features-open-reference qiime2 vsearch dereplicate-sequences qiime2 vsearch fastq-stats qiime2 vsearch merge-pairs qiime2 vsearch uchime-denovo qiime2 vsearch uchime-ref

CheckV end to end

hicBuildMatrix

hicCorrectMatrix

hicCorrelate

hicPlotDistVsCounts

hicSumMatrices

OMERO get Object

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

Count Covariates

Convert BAM to BigWig Convert BAM to coordinate-sorted BAM Convert BAM to queryname-sorted BAM Convert BED to Feature Location Index Convert BED to GFF Convert BED, GFF, or VCF to BigWig Convert BGZ VCF to tabix Convert Bam to Bai Convert BedGraph to BigWig Convert BigWig to Wiggle Convert Biom datasets Convert CML to SMILES Convert CRAM to BAM Convert CSV to tabular Convert FASTA to 2bit Convert FASTA to Bowtie base space Index Convert FASTA to Bowtie color space Index Convert FASTA to Tabular Convert FASTA to fai file Convert FASTA to len file Convert FASTQ files to seek locations Convert GFF to BED Convert GFF to Feature Location Index Convert GFF to Interval Index Convert GRO to PDB Convert Genomic Intervals To BED Convert Genomic Intervals To Coverage Convert Genomic Intervals To Strict BED Convert Genomic Intervals To Strict BED12 Convert Genomic Intervals To Strict BED6 Convert InChI to MOL Convert Interval to BGZIP Convert Interval to tabix Convert Len file to Linecount Convert MAF to Fasta Convert MAF to Genomic Intervals Convert MOL2 to MOL Convert PDB to GRO Convert Parquet to csv Convert Picard Interval List to BED6 Convert Ref taxonomy to Seq Taxonomy Convert SAM to BAM without sorting Convert SAM to BigWig Convert SMILES to MOL Convert Wiggle to BigWig Convert Wiggle to Interval Convert XTC, DCD, and TRR Convert bz2 compressed file to uncompressed. Convert compressed and uncompressed BCF files Convert from bigBed to ascii bed format. Convert gz compressed file to uncompressed. Convert lped to fped Convert lped to plink pbed Convert neostore.zip files to neostore Convert plink pbed to ld reduced format Convert plink pbed to linkage lped Convert tabular to CSV Convert tabular to dbnsfp Convert uncompressed file to compressed OpenBabel converter for molecular formats SMILES to SMILES Unpack archive to directory

chromap