European Galaxy tools (3706 and counting)

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Get Data

Get sequences by Ensembl ID IEDB Protein Database Downloader Faster Download and Extract Reads in FASTQ Download and Extract Reads in BAM NCBI Accession Download Download and Generate Pileup Format UniProt Get species occurrences data Unipept NCBI ESearch NCBI EGQuery NCBI ECitMatch NCBI EPost NCBI ELink NCBI EInfo NCBI ESummary NCBI EFetch UniProt 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 NCBI Datasets Gene NCBI Datasets Genomes Upload File SEEK test pysradb search Download and Extract Reads in FASTQ IMPC MaveDB Argo data access OBIS occurences Adds environment variables AquaINFRA Importer SdmPredictors List Layers Retrieve bold Copernicus Marine Data Store fastq-dl 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 Export datasets

Collection Operations

Split file Split file Collapse Collection Filter null elements Unzip Extract element identifiers Column join Pick parameter value Unzip collection Zip collections Filter failed datasets Filter empty datasets Flatten collection Merge collections Relabel identifiers Filter collection Sort collection Harmonize two collections Flat Cross Product Nested Cross Product Tag elements Apply rules Build list Extract dataset Duplicate file to collection

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

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 Filter Tabular JQ cast Replace Text melt Rebase GFF3 features Cluster Text reformatting Remove columns Sort Column Order tac Advanced Cut Join Concatenate datasets Multi-Join Unique lines 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 Subtract Whole Dataset Unique Add column Split by group Concatenate multiple datasets Excel to Tabular Number lines 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 AGAT wigtobigwig BAM BED GFF coverage bigWigs UniProt BED-to-GFF GFF-to-BED MAF to BED MAF to Interval MAF to FASTA SFF converter BED-to-bigBed

Filter and Sort

Filter FASTA Column arrange XPath Filter sequences by ID Sub-sample sequences files find in reference Bigwig outliers to bed features GffCompare 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 Glimmer to GFF Tabular-to-FASTA FASTA-to-Tabular Tabular to FASTQ GFA to FASTA msconvert Extract MAF blocks CrossMap Wig idconvert msconvert Subset Peak List CrossMap VCF CrossMap GFF CrossMap BED Thermo Stitch Gene blocks CrossMap BAM mz to sqlite bed to protein map Convert gffCompare annotated GTF to BED Map peptides to a bed file Convert Resize coordinate window gffread msms_extractor bax2bam Image Montage Convert image format Create InterMine Interchange idconvert Convert GTF to BED12 twoBitToFa idpQuery Convert BAM to ScIdx bigWigToBedGraph Convert BAM CrossMap region samtools BAM to CRAM ab1 to FASTQ converter hictk Compress file(s) xmlstarlet MGA to GFF3 Fix tRNA model Genbank to Five Column Format GFF3 to GenBank Split GFF3+Fasta into separate parts (CPT) Genbank to GFF3: Compare two images PacBio bam2fastx Add metadata Normalize Subset Summarize sample or observation data Create a BIOM table ToolDistillator ToolDistillator Summarize mafToAxt axtChain netToAxt netFilter chainNet wigtobigwig 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 BED-to-bigBed Convert genome coordinates

FASTA/FASTQ

BBTools: BBNorm FastQC Trim Galore! filtlong Select high quality segments Cutadapt Fasta Statistics FASTQE RNA-seq Rcorrector UMI-tools count UMI-tools deduplicate UMI-tools extract UMI-tools group UMI-tools whitelist fastp faSplit FASTQ splitter Filter sequences by mapping Pear Calculate sequence complexity SeqKit statistics SeqKit fx2tab gfastats AdapterRemoval: remove adapter sequences SeqKit locate Fasta regular expression finder BBTools: BBMerge FASTA Width RNA/DNA Draw quality score boxplot Quality format converter Filter by quality FASTQ to FASTA Remove sequencing artifacts Barcode Splitter Clip Collapse Draw nucleotides distribution chart Compute quality statistics Rename sequences Reverse-Complement Trim sequences Remove Description Trimmomatic 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 BBTools: Tadpole BBTools: BBduk Merging paired-end Illumina reads (SeqPrep) rasusa NCBI FCS GX ART 454 ART Illumina ART SOLiD Falco SeqKit translate SeqKit sort Length Distribution FASTQ Groomer Combine FASTA and QUAL Compute sequence length Filter FASTQ FASTQ Masker FASTQ de-interlacer Manipulate FASTQ FASTQ joiner FASTQ interlacer FASTQ to Tabular FASTQ Trimmer FASTQ to FASTA FASTQ Summary Statistics Tabular to FASTQ Build base quality distribution Concatenate FASTQ Quality Trimmer SeqKit Head Sickle Filter sequences by length FASTA-to-Tabular Tabular-to-FASTA Exonerate FLASH mQC Get crosslinked nucleotides 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 FASTA Merge Files and Filter Unique Sequences Thread nucleotides onto a protein alignment (back-translation) PRINSEQ lighter fastq-join Split Fasta Split Fasta Convert Compute quality statistics Draw quality score boxplot

Quality Control

MultiQC QualiMap Counts QC FASTQ info

SAM/BAM

Sambamba sort 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 Filter BAM Samtools calmd Samtools phase BamHash Split BAM into paired- and single-end Split BAM by reference Split BAM by reads mapping status Split BAM by read tag value Sambamba markdup Sambamba merge Sambamba merge BamUtil diff Samtools ampliconclip revertR2orientationInBam Split mosdepth Analysis of artifacts with Tasmanian Sambamba flagstat

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 bedtools Convert from BAM to FastQ Create a BedGraph of genome coverage Merge BedGraph files Create a histogram of genome coverage bedops sort-bed

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

Clair3 Porechop 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 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 m6anet

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Common Genomics Tools

Operate on Genomic Intervals

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

multiGSEA DeepARG short reads DeepARG predict Sanntis biosynthetic gene clusters CryptoGenotyper Augustus SnpSift GeneSets tRNA and tmRNA Annotate with DGI psortb RXLR Motifs Promoter 2.0 TMHMM 2.0 Annotate with DGI HHsearch sistr_cmd seq2HLA Busco OptiType ABRicate Summary TB-Profiler Profile MITOS MITOS2 Glimmer ICM builder Glimmer3 Glimmer3 goseq Maker TB Variant Report TB Variant Filter annotateMyIDs Train Augustus hmmsearch hmmemit hmmalign nhmmscan jackhmmer phmmer hmmscan hmmfetch alimask hmmconvert hmmbuild nhmmer MOB-Recon MOB-Typer lorikeet spoligotyping SpoTyping RepeatModeler ChIPseeker RepeatMasker scanMotifGenomeWide annotatePeaks findMotifsGenome Converts GTF to Annotations file for Homer Prokka hAMRonize hamronize summarize: Funannotate assembly clean Sort assembly Funannotate predict annotation Funannotate compare Funannotate functional Roary List spaln parameter tables Spaln: align cDNA or Protein to genome GECCO InterProScan TRANSIT Gumbel TRANSIT Resampling TRANSIT Tn5Gaps TRANSIT HMM KofamScan legsta SignalP 3.0 WoLF PSORT Antismash TEfinder Gubbins ISEScan Miniprot align netboxr PlasmidFinder Miniprot index Red Integron Finder edta Bakta CPAT GffCompare PfamScan pharokka findMotifs MLST MLST List Braker genome annotation Get open reading frames (ORFs) or coding sequences (CDSs) GFF3 Add Gene to CDS GFF3 Add Gene to CDS for Sixpack Shine Find GFF3 Feature Type Filter GFF3 Filter: Require Phage Start Remove Annotation Feature Prep GFF3 Input for Apollo Glimmer3 to GFF3 AGAT BRAKER3 Helixer Interrupted gene detection tool GFF3 Feature Sequence Export Identify Lipoboxes Renumber GenBank Genes Genome Editor Phage QC Annotation Table Rebase GFF3 features Gff3 Filter: Require SD AMRFinderPlus RepeatExplorer (clustering) DeepSig Build a GeneNoteBook TSEBRA WindowMasker mkcounts WindowMasker ustat OrthoFinder TAPScan Classify AEGeAn CanonGFF3 AEGeAn LocusPocus AEGeAn ParsEval AEGeAn GAEVAL Fasta Translate OMArk krocus MirMachine Prodigal Gene Predictor compleasm abriTAMR ChewBBACA AlleleCall chewBBACA AlleleCallEvaluator chewBBACA CreateSchema chewBBACA DownloadSchema chewBBACA ExtractCgMLST chewBBACA JoinProfiles chewBBACA NSStats chewBBACA PrepExternalSchema STR to bed Protein Blast Grouping Related Prophages tool Intersect and Adjacent argNorm EVidenceModeler Groot TETyper ectyper staramr PPanGGOLiN all PPanGGOLiN MSA hicBuildMatrixMicroC autoBIGS.cli Table to GFF3 progressiveMauve Convert XMFA to gapped GFF3 Genbank to GFF3 Exonerate FastANI fargene KOBAS Annotate KOBAS Identify Convert GFF3 gProfiler SNPense gProfiler Random gProfiler GOSt gProfiler Orth gProfiler Convert ABRicate ABRicate List BlastXML to gapped GFF3 Compute socru Train SNAP Map annotation ids fgsea GOSlimmer GOEnrichment Genome annotation statistics Metagenome Contributions Format Compare BIOM tables Predict Metagenome Categorize tRNA prediction TransTermHP estimate-energy fix-fasta-headers filter-annotated-entries add-read-counts find-boxes filter-by-energy extract-boxed-sequences segmentation-fold Filter with SortMeRNA ProbMetab Tool LC/MS matching Nucleosome Predictions miRanda DotKnot Nucleotide subsequence search GotohScan

Multiple Alignments

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

Assembly

rnaviralSPAdes Meryl FastK Logex FastK Flye Hifiasm 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 Quast miniasm ABySS Create assemblies with Unicycler IDBA-UD IDBA-HYBRID SPAdes VelvetOptimiser pilon WTDBG2 metaSPAdes DISCO rnaSPAdes Meryl Assemble with MIRA v3.4 rnaQUAST velvetg Edena (assembling) Edena (overlapping) SOPRA with prebuilt contigs SSAKE CRISPR Recognition Tool detect CRISPR sequences GenomeScope PretextMap Bionano Hybrid Scaffold Filter and merge MitoHiFi Raven RagTag TGS-GapCloser HyPo plasmidSPAdes metaviralSPAdes metaplasmidSPAdes coronaSPAdes biosyntheticSPAdes LINKS gfastats Merqury YAHS velvetg velveth cap3 Smudgeplot Hapo-G Get organelle from reads minipolish Cactus Cactus: export instaGRAAL necat BiSCoT Hifiasm_meta BlobToolKit NextDenovo Get annotated regions from genbank files (getorganelle) Consensus sequence from aligned FASTA verkko velveth Pairtools dedup Pairtools parse Pairtools split Pairtools sort Pairtools Stats FastK Histex Meryl Meryl Meryl Meryl Meryl Meryl Merqury histogram plot Pretextgraph Reago RefSeq Masher Contains RefSeq Masher Matches ERGA Assembly Reporting Tool (EAR)

Mapping

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

Variant Calling

BBTools: call variants CNVkit Target CNVkit Genemetrics CNVkit Theta CNVkit Call Naive Variant Caller (NVC) FreeBayes BamLeftAlign bcftools split-vep Variant Annotator SnpSift Intervals SnpEff eff: SnpSift Annotate SnpSift Filter SnpSift CaseControl Get homopolymer run length snippy-core snippy snippy-clean_full_aln sansa annotate JasmineSV Iris bcftools mpileup bcftools view bcftools stats bcftools roh bcftools reheader bcftools query bcftools isec bcftools gtcheck bcftools filter bcftools convert to vcf bcftools convert from vcf bcftools annotate Beagle LUMPY preprocessing LUMPY seqwish DeepVariant GATK4 Mutect2 bcftools cnv Control-FREEC KING VarDict Delly cnv Delly classify Delly long-read (lr) Delly call Delly merge Delly filter ARTIC guppyplex ARTIC minion plink bcftools concat VarScan mpileup bcftools merge pharmCAT CNVkit Heatmap CNVkit Batch faToVcf Strelka Germline Strelka Somatic bcftools consensus vcfanno DCS mutations to tags/reads: DCS mutations to SSCS stats: Call specific mutations in reads: SnpSift Filter Lofreq filter Call variants cuteSV SnpEff eff: Realign reads Add LoFreq alignment quality scores Insert indel qualities odgi viz odgi build vg view vg deconstruct vg convert 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 call bcftools norm bcftools csq bcftools frameshifts bcftools color-chrs SNP distance matrix Tag pileup frequency Finds SNP sites ExomeDepth SnpEff build: VarScan somatic basil SnpSift Intervals SnpSift rmInfo SnpSift Variant Type SnpSift Annotate SnpSift CaseControl SnpEff chromosome-info: SnpSift Extract Fields SnpSift vcfCheck bcftoolsView VT normalize SnpEff databases: SnpSift GeneSets SnpSift dbNSFP SnpSift dbNSFP SnpEff download: VarScan copynumber VarScan SnpEff Ensembl CDS SnpEff to Peptide fasta Predict variant effects breseq Convert VCF to MAF CNVkit Access CNVkit Antitarget CNVkit Autobin CNVkit Coverage CNVkit Diagram CNVkit Fix CNVkit Breaks CNVkit Reference CNVkit Scatter CNVkit Segment CNVkit Segmetrics CNVkit Sex CNVkit Export BED CNVkit Export CDT CNVkit Export JTV CNVkit Export Nexus Basics CNVkit Export Nexus OGT CNVkit Export SEG CNVkit Export VCF CNV VCF2JSON bcftools setGT bcftools setGT Frameshift Deletions Checks Beacon2 CSV2XLSX Beacon2 PXF2BFF Beacon2 VCF2BFF Manta CNV Phenopacket hgvsParseR Beacon2 Analyses Beacon2 Biosamples Beacon2 Bracket Beacon2 CNV Beacon2 Cohorts Beacon2 Datasets Beacon2 Gene Beacon2 Import Beacon2 Individuals Beacon2 Range Beacon2 Runs Beacon2 Sequence sniffles

Genome editing

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

RNA-Seq

blockbuster

RNA Analysis

CEMiTool Filter Combined Transcripts eXpress Cuffmerge Cufflinks Cuffdiff Cuffcompare Remove Unwanted Variation FEELnc featureCounts 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 Salmon quantmerge GLASSgo IntaRNA Kallisto pseudo Kallisto quant edgeR Cross-contamination Barcode Filter 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 Gene Body Coverage (BAM) Fit a BUM model Identify optimal scoring subnetwork Calculate a Heinz score ssHMM pizzly RCAS Gene Body Coverage (Bigwig) RPKM Saturation Infer Experiment RNA fragment size Transcript Integrity Number Junction Saturation FPKM Count Read Distribution RNAcode Junction Annotation Inner Distance RNAz RNAshapes RNAfold IDR RNAcofold RNAalifold Deletion Profile Read NVC BAM/SAM Mapping Stats Read Duplication Read GC Insertion Profile BAM to Wiggle Clipping Profile Read Quality Hexamer frequency Mismatch Profile 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 RNAformer GenomicSuperSignature barrnap Arriba Draw Fusions Arriba Get Filters Arriba CIRCexplorer2 riboWaltz riboWaltz-plot Train a CheRRI model using RRIs miRNAture Evaluation of RRIs using CheRRI IsoformSwitchAnalyzeR Sleuth Trinity Stats CMsearch deoverlap PsiCLASS RBPBench BREW3R.r Seurat Preprocessing Seurat Integrate Seurat Run Dimensional Reduction Seurat Create Seurat Visualize Seurat Data Management Seurat Find Clusters Sfold

Peak Calling

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

Epigenetics

Filter SEACR MOABS Minfi Preprocess Quantile Minfi Rset Minfi Drop SNPs Minfi Mset Minfi Read 450k Minfi Preprocess Funnorm Minfi DMP 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 Hicup Truncater Hicup Pipeline Hicup Filter Hicup Digester Hicup Deduplicator EpiCSeg - Chromatin segmentation Hicup Mapper hifive cooler_makebins cooler csort with tabix cooler_cload_tabix cooler_balance Hicup to juicer converter Cooler zoomify

Phylogenetics

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

Phenotype Association

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

Single-cell

drug2cell MuData import and export muon filter and normalize CSIDE Manipulate AnnData Import Anndata Export AnnData Manipulate Expression Set Object Inspect AnnData Loom operations DropletUtils DropletUtils Read10x DropletUtils emptyDrops Alevin Scanpy filter Scanpy Inspect and manipulate Scanpy normalize Scanpy plot Scanpy remove confounders Slice Image Scanpy cluster, 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 scran_normalize CITE-seq-Count Sinto barcode Sinto fragments Build count matrix scATAC-seq Preprocessing Cluster, embed and annotate RCTD muon plot muon Cluster, analyze, and embed multimodal data anndata2ri velocyto CLI baredSC 1d baredSC 2d Combine multiple 1D Models Combine multiple 2D Models SCEasy Converter SnapATAC2 Plotting SnapATAC2 Clustering SnapATAC2 Preprocessing SnapATAC2 peaks and motif InferCNV COSG Selection Evaluation

Spatial Omics

Perform segmentation of multiplexed tissue data 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 Picard Collect Sequencing Artifact Metrics SAM/BAM Alignment Summary Metrics Add or Replace Groups BAM Index Statistics Insertion size metrics Estimate Library Complexity Paired Read Mate Fixer CollectHsMetrics

deepTools

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

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 EMBOSS: needleall EMBOSS: needle

NCBI Blast

BLAST top hit descriptions Diamond Diamond makedb Diamond view BBTools: call variants BLAST XML to tabular NCBI get species taxids 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 Magic-BLAST: map large RNA or DNA sequences BLAST Reciprocal Best Hits (RBH)

HiCExplorer

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

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

MetaPhlAn dada2: assignTaxonomy and addSpecies Binette Phyloseq: plot alpha diverstiy measure Add Rank Names to Phyloseq Object Biobox add taxid Create phyloseq object Fairy sketch dRep compare Decontam Kraken2 dada2: makeSequenceTable dada2: plotQualityProfile dada2: mergePairs dada2: plotComplexity dada2: learnErrors dada2: dada dada2: removeBimeraDenovo dada2: filterAndTrim MetaEuk Easy Predict staramr LAST-train MT2MQ VSearch search LASTal dRep dereplicate LASTdb LAST-split MAF-convert mash screen MetaGeneAnnotator mash sketch sixgill merge sixgill filter sixgill build sixgill makefasta CAT bins 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 Kraken-translate CAT add_names CAT summarise CAT prepare MaxBin2 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 Format MetaPhlAn2 VALET GDCWebApp Salmonella Subtyping Nonpareil Format MetaPhlAn2 Merge Krona pie chart metagenomeSeq Normalization Generate heatmap Kraken-filter Kraken taxonomic report Convert Kraken Scoary jellyfish HUMAnN Barplot Join (merge) Reduce Regroup Rename features Renormalize Split a HUMAnN table Split Unpack pathway abundances Extract the marker sequences and metadata Customize the marker sequences and metadata LotuS2 InStrain Profile InStrain Compare CAMI AMBER add length column metabuli classify CAMI AMBER convert to biobox CoverM contig CoverM genome Bracken 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 Phyloseq: plot ordination 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 Kleborate Polypolish SemiBin: Contig annotations SemiBin SemiBin: Train SemiBin: Generate sequence features SemiBin: Group the contigs SemiBin: Concatenate fasta files 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 Krakentools: Convert kraken report file Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) Krakentools: Calculates alpha diversity Krakentools: Convert kraken report file Krakentools: Combine multiple Kraken reports Krakentools: Extract Kraken Reads By ID dada2: sequence counts dada2: primer check Phyloseq: Bar Chart Create phyloseq object Fairy coverage checkm2 Combine MetaPhlAn and HUMAnN outputs MAPseq SeqSero2 BiG-SCAPE virAnnot Blast2tsv virAnnot OTU virAnnot Rps2tsv SIRIUS-CSI:FingerID MetaWRAP GTDB-Tk Classify genomes qiime2 dada2 denoise-ccs CAMI AMBER taxpasta geNomad Metagenomics toolkit Original Metadata Metagenomics toolkit Bulk Download Name2taxid NCBI-GTDB map Merge mOTUs_profiler tiara VIBRANT VirSorter Profile2CAMI

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

Data and Metadata Management

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

Virology

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

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Proteomics, Metabolomics, Chemistry

Proteomics

FragPipe - Academic Research and Education User License (Non-Commercial) MaxQuant MSstatsTMT MSstats 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 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 SpecLibCreator MapAlignerSpectrum 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 MSI classification AccurateMassSearch DatabaseFilter DeMeanderize FeatureFinderSuperHirn IDFileConverter OpenSwathMzMLFileCacher OpenSwathRewriteToFeatureXML IDPosteriorErrorProbability 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 MALDIquant peak detection 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 MALDIquant preprocessing 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 bioconductor-scp RTPredict PTPredict InspectAdapter InclusionExclusionListCreator LowMemPeakPickerHiResRandomAccess IDDecoyProbability RNPxl AdditiveSeries idpQuery TopPerc Protease prediction Create Decoy Database (reverse) Morpheus FastaCLI Identification Parameters Diffacto ProteomIQon MzMLToMzLite ProteomIQon PeptideDB ProteomIQon PeptideSpectrumMatching ProteomIQon PSMStatistics ProteomIQon ProteinInference MaxQuant (using mqpar.xml) 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 MaxQuant Phosphopeptide Preprocessing MaxQuant Phosphopeptide ANOVA QuPath ROI Splitter PepQuery2 PepQuery2 Show Sets PepQuery2 index calisp DIA-NN eggNOG Mapper eggNOG Mapper SageAdapter OpenMSInfo JSONExporter Zeiss laser-capture microdissection converter

Metabolomics

Calculate flux distribution table scipy interpolate 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 MetFrag 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 Transformation 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 Anova Multivariate Biosigner Generic_Filter Quality Metrics metaMS.runGC Multilevel Check Format Determine_batch_correction Batch_correction MassBank spectrum searches ProbMetab Tool Univariate Heatmap CAMERA.combinexsAnnos proFIA NMR_Bucketing NMR_Normalization NMR spectra alignment NMR spectra alignment xcms plot raw xcms plot eic xcms refineChromPeaks (refine) Isoplot: Generate plots from isocor output recetox-aplcms - generate feature table recetox-aplcms - recover weaker signals recetox-aplcms - correct time recetox-aplcms - compute clusters recetox-aplcms - remove noise recetox-aplcms - merge known table recetox-aplcms - compute template recetox-aplcms - align features RMassBank BioTransformer MSMetaEnhancer RIAssigner RAMClustR RAMClustR define experiment recetox-xMSannotator matchms convert matchms filtering matchms fingerprint similarity matchms scores formatter matchms metadata export matchms metadata match matchms networking matchms similarity matchms spectral similarity matchms split library WaveICA dimet abundance plot dimet differential analysis dimet differential multigroup analysis dimet enrichment plot dimet isotopologues plot dimet metabologram dimet pca analysis dimet pca plot dimet timecourse analysis MZMine batch matchms subsetting matchms metadata merge matchms add key matchms remove key RECETOX MsFinder dimet bivariate analysis use theoretical m/z values RIAssigner init from comment tracegroomer SIRIUS-CSI:FingerID isolib GC derivatization matchms remove spectra Skyline2Isocor: converting skyling outputs into IsoCor inputs bioconductor-msnbase smooth mz bioconductor-msnbase smooth chromatogram bioconductor-msnbase centroid table arithmetics table column transformations table rename column Get exchange bounds table rename columns via regex Pathway visualization Make GEM quality report Rename Annotated Feature spec2vec similarity spec2vec model training MFAssignR SNplot MFAssignR HistNoise MFAssignR KMDNoise MFAssignR IsoFiltR MFAssignR MFAssign MFAssignR MFAssignCHO MFAssignR Recal MFAssignR RecalList rcx-tk MFAssignR FindRecalSeries MS2DeepScore Configuration Generator MS2DeepScore Similarity MS2DeepScore Model Training MS target screening mixmodel

ChemicalToolBox

MDS Scatter Plot Conformer calculation Online data Generate MD topologies for small molecules PubChem Assay Downloader Search ChEMBL database AnteChamber Convert Parameters Open Molecule Generator ParmChk2 Prepare receptor Trajectory select and merge MDTraj file converter MMPBSA/MMGBSA Score docked poses using SuCOS GROMACS solvation and adding ions GROMACS production simulation dcTMD friction correction Slice MD trajectories Calculate the box parameters using RDKit Drug-likeness GROMACS simulation Pharmacophore alignment Pharmacophore GROMACS structure configuration dpocket fpocket Create GROMACS index files GROMACS initial setup GROMACS energy minimization Merge GROMACS topologies Modify/convert and concatate GROMACS trajectories Extract energy components with GROMACS Create GROMACS position restraints files GROMACS Radius of Gyration Convert Amber topology and coordinate files to GROMACS format VINA Docking Build tLEaP Alphafold 2 Adding New Topology Information Extracting Topology Information GROMACS copy file PDBFixer GROMACS check GROMACS RMSD calculation GROMACS RMSF calculation xtb molecular optimization Remove coordination complexes QCxMS neutral run QCxMS production run QCxMS get results Convert Qiskit’s XYZ files to PULCHRA recontruction of all atom proteins Align structures and compute relative RMSDs Compound search Compute physico-chemical properties Visualisation Spectrophores search Compound conversion Substructure Search Hierarchical clustering Extract clusters of MD trajectories Extract RMSD distance matrix data Add hydrogen atoms Remove counterions and fragments ChEMBL structure pipeline 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 Angle Analysis APoc smina Enumerate changes Extract values from an SD-file Calculate molecular descriptors PubChem Download PubChem Assay Downloader Prepare ligand Remove duplicated molecules Filter Remove small molecules Prepare ligands for docking Descriptors 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 OpenDUck chunk Run OpenDUck XChem TransFS pose scoring Molecule to fingerprint NxN clustering Taylor-Butina clustering SDF to Fingerprint fastpca RDConf: Low-energy ligand conformer search Alchemical Analysis Hydrogen Bond Analysis using VMD PCA visualization RMSF Analysis PCA RMSD Analysis DCCM analysis 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 Fragmenter Merging ChEMBL structure pipeline

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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 SaQC Create a model to recommend tools Wavelet variance GraphEmbed Plot actual vs predicted curves and residual plots Plot confusion matrix, precision, recall and ROC and AUC curves Rolling window Nearest Neighbors Classification IWTomics Plot with Threshold IWTomics Test IWTomics Load Sequence composition RGCCA Statistical hypothesis testing Distance matrix-based hierarchical clustering Summary Statistics Count

Machine Learning

Tabular data prediction using TabPFN 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 FLUX To categorical MCL virhunter decontaminator DeepMicro Label encoder Colorize label map Prediction of Breast Cancer (BC) Random Forest model Speech to Text Flexynesis chatGPT

Graph/Display Data

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

Muon Spectroscopy

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

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Miscellaneous Tools

Evolution

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

Motif Tools

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

Test Tools

Quality Control FastP Bracken QUAST Analysis and FASTA Generator MLST, AMRfinder, and STARamr Analysis ChIPpeakAnno annoPeaks Cluster Profiler Bitr Cluster Profiler GO NetCDF to Zarr zeppelin Concatenate Icenet Data Icenet Forecast Preprocess Icenet Data create API requests for Icenet Data Visualize Icenet Forecast 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 bwtool-lift Calculate protein properties Base Count Codon count GenBank and EBML Extract sequences from GenBank GFF converter Sequence converter Translate nucleotides RNALfoldz

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 AquaINFRA OGC API Processes Run interpolation OTB.BandMath OTB.MeanShiftSmoothing Terrabyte OGC API Processes Zoo Project OGC API Processes Hirondelle CRIM OGC API Processes

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

QCV harmonizer 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 Land cover degradation

Apollo

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

Imaging

Perform color deconvolution or transformation Run generalist cell and nucleus segmentation OMERO IDs Run CellProfiler pipeline Starting Modules ColorToGray Tile TrackObjects OverlayOutlines ConvertObjectsToImage DisplayDataOnImage EnhanceOrSuppressFeatures ExportToSpreadsheet GrayToColor IdentifyPrimaryObjects MaskImage MeasureGranularity MeasureImageAreaOccupied MeasureImageIntensity MeasureImageQuality MeasureObjectIntensity MeasureObjectSizeShape MeasureTexture RelateObjects SaveImages ImageMath Perform affine image registration (landmark-based) Performs projective transformation Perform affine image registration (intensity-based) Perform wavelet transformation on 3D-image stack Convert binary image to EDM Skeletonize Find edges Add shadow effect Enhance contrast Find maxima Perform segmentation using watershed transformation Apply raw transformation Operate on pixels Apply elastic transformation Download IDR/OMERO Extract top view from whole-slide image Image Converter 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 image 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 Show image info Visualize detections Threshold image Perform histogram equalization Convert image format Extract image features Permutate image axes Convert label map to points (center of masses) Convert point coordinates to label map Concatenate images or channels Scale image Merge neighbors in label map Convert binary image to label map Filter label map by rules Apply anisotropic diffusion Filter 2-D image Switch axis coordinates Convert binary image to points (point coordinates) Count objects in label map Compute image features Performs projective transformation with/without labels Evaluate segmentation Convert binary image to points (center of masses) Slice image into patches Split label map using morphological operators Remove image background Colocalization Overlay Overlay Segmentation Mask Perform segmentation in densely packed 3-D volumetric images Perform curve fitting Perform linking in time series (nearest neighbors) Perform 2-D spot detection Overlay images Run CellProfiler pipeline Compute image segmentation and object detection performance measures Perform gating Vitessce Analyze and visualize spatial multi-omics data Rename OME-TIFF channels Process single-cell intensities Perform segmentation using deformable shape models Perform segmentation using region-based fitting of overlapping ellipses OMERO get IDs OMERO get Object FTP Link for Bioimage Archive Process image using a BioImage.IO model Split image along axes Wound healing scratch assay Convert to OME-Zarr Compute Voronoi tessellation Apply a morphological operation Process images using arithmetic expressions Compute image orientation Convert label map to binary image Colorize label map Convert single-channel to multi-channel image Create spatial scatterplot Analyze and visualize spatial multi-omics data Convert Anndata to CSV

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

Ecoregionalization

BRT tool prediction TaxaSeeker EcoMap ClusterEstimate ClaraClust GeoNearestNeighbor

Indicators from geometric mean

Make a map with a shapefile Geometric means Bar plot DIVAnd

Astronomy

astropy fits2bitmap astropy fits2csv astropy fitsinfo Astronomical Archives (IVOA) SGWB HESS CTA

Interactive tools

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

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

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

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

QIIME 2

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-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-distance-matrix qiime2 diversity filter-alpha-diversity 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 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 taxa barplot qiime2 taxa collapse qiime2 taxa filter-seqs qiime2 taxa filter-table 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 qiime2 tools export qiime2 tools import qiime2 deblur denoise-16S QIIME vizualisation extractor qiime2 vizard boxplot qiime2 stats collate-stats qiime2 stats wilcoxon-srt qiime2 stats plot-rainclouds qiime2 stats facet-across qiime2 stats facet-within qiime2 stats prep-alpha-distribution qiime2 rescript get-bv-brc-genome-features qiime2 rescript get-bv-brc-genomes qiime2 rescript get-bv-brc-metadata qiime2 tools import-fastq

Data Managers

CheckV end to end

Metagenomic Analysis

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

GATK Tools

Count Covariates

XAS (X-ray Absorption Spectroscopy)

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

Built-in Converters

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