European Galaxy tools (3456 and counting)

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Get Data

Faster Download and Extract Reads in FASTQ Download and Extract Reads in FASTQ Download and Extract Reads in BAM OBIS occurences Argo data access MaveDB IEDB Protein Database Downloader 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 sequences by Ensembl ID Get gene tree by Ensembl ID IMPC Adds environment variables NCBI Datasets Gene NCBI Datasets Genomes Get features by Ensembl ID Search ENA data Retrieve ENA data Retrieve ENA taxon data Retrieve an analysis report Retrieve a run report EBI Search DoRiNA Search Download run data EGA Download Client Upload File SEEK test pysradb search UCSC Main UCSC Archaea NCBI Datasets Genomes downloads EBI SRA SRA Get Microbial Data BioMart BioMart CBI Rice Mart GrameneMart modENCODE fly InterMine Flymine modENCODE modMine MouseMine Ratmine YeastMine metabolicMine modENCODE worm WormBase ZebrafishMine EuPathDB HbVar OmicsDI

Send Data

ENA Upload tool cURL Send to cloud Export datasets

Collection Operations

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

Text reformatting Concatenate datasets Advanced Cut Join Replace Search in textfiles Select first Multi-Join Number lines Create text file Replace Text Replace Text Text transformation Sort Sort a row Unique lines tac Select last Unfold Unique 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 Query Tabular Replace chromosome names SQLite to tabular Filter Tabular JQ cast melt Cluster Rebase GFF3 features Remove columns Sort Column Order 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 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

wigtobigwig Convert a 10X BAM file to FASTQ Convert Glimmer to GFF AGAT BED-to-GFF GFF-to-BED MAF to BED MAF to Interval MAF to FASTA SFF converter BED-to-bigBed

Filter and Sort

Filter sequences by ID Filter FASTA Column arrange Sub-sample sequences files XPath find in reference 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

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

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Genomic File Manipulation

Convert Formats

Convert Convert BAM Image Montage Compare two images gffread Convert image format idpQuery Tabular-to-FASTA FASTA-to-Tabular Tabular to FASTQ GFA to FASTA Thermo msconvert Extract MAF blocks CrossMap Wig CrossMap VCF CrossMap GFF CrossMap BED Stitch Gene blocks CrossMap BAM mz to sqlite bed to protein map Convert gffCompare annotated GTF to BED Map peptides to a bed file Resize coordinate window msms_extractor bax2bam Create InterMine Interchange samtools BAM to CRAM PacBio bam2fastx hictk idconvert msconvert Subset Peak List idconvert Convert GTF to BED12 twoBitToFa Convert BAM to ScIdx bigWigToBedGraph CrossMap region ab1 to FASTQ converter 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: 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

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

Quality Control

MultiQC QualiMap Counts QC FASTQ info

SAM/BAM

Operate on and transform BAM mosdepth Samtools ampliconclip 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 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 Split BAM by reads mapping status Split BAM into paired- and single-end Split BAM by reference Split BAM by read tag value Samtools phase BamHash VarScan mpileup VarScan Somatic VarScan Somatic BamUtil diff revertR2orientationInBam Split

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 VCFtoTab-delimited: VCFtoTab-delimited: VCFgenotype-to-haplotype: VcfAllelicPrimitives: VCFannotate: VCFannotateGenotypes: VCF-BEDintersect: VCFgenotypes: VCFcheck: VCFcombine: VCFcommonSamples: VCFdistance: VCFbreakCreateMulti: Compare Annotate Slice VCF Subset

Nanopore

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

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Common Genomics Tools

Operate on Genomic Intervals

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

Fetch Sequences / Alignments

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

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Genomics Analysis

Annotation

legsta krocus OMArk jackhmmer hmmemit hmmalign multiGSEA TSEBRA annotateMyIDs Fasta Translate BRAKER3 AEGeAn LocusPocus Bakta AGAT compleasm MITOS2 Build a GeneNoteBook ISEScan Funannotate compare WindowMasker mkcounts WindowMasker ustat nhmmer DeepSig Sort assembly Funannotate assembly clean RepeatExplorer (clustering) Funannotate predict annotation Busco OptiType Prokka Roary TB-Profiler Profile hmmbuild hmmscan phmmer nhmmscan hmmsearch KofamScan Table to GFF3 MOB-Recon MOB-Typer ectyper sistr_cmd MITOS Antismash ChIPseeker progressiveMauve Convert XMFA to gapped GFF3 MLST List MLST Genbank to GFF3 Exonerate seq2HLA FastANI TRANSIT Tn5Gaps TRANSIT Resampling TRANSIT HMM TRANSIT Gumbel TETyper Train Augustus Augustus fargene KOBAS Annotate KOBAS Identify Convert GFF3 gProfiler SNPense gProfiler Random gProfiler GOSt gProfiler Orth gProfiler Convert ABRicate ABRicate List BlastXML to gapped GFF3 Maker Compute socru goseq Red Train SNAP Map annotation ids fgsea Spaln: align cDNA or Protein to genome GOSlimmer GOEnrichment Genome annotation statistics psortb SignalP 3.0 Promoter 2.0 TMHMM 2.0 RXLR Motifs WoLF PSORT Metagenome Contributions Format Compare BIOM tables Predict Metagenome Categorize tRNA prediction tRNA and tmRNA TransTermHP estimate-energy fix-fasta-headers filter-annotated-entries add-read-counts find-boxes filter-by-energy extract-boxed-sequences segmentation-fold Gubbins Filter with SortMeRNA ProbMetab Tool LC/MS matching Nucleosome Predictions OrthoFinder miRanda DotKnot RepeatModeler alimask AMRFinderPlus Funannotate functional hmmconvert CPAT TAPScan Classify AEGeAn CanonGFF3 AEGeAn ParsEval Intersect and Adjacent Helixer Integron Finder hmmfetch hamronize summarize: hAMRonize MirMachine abriTAMR Miniprot align Miniprot index Prodigal Gene Predictor AEGeAn GAEVAL Nucleotide subsequence search GotohScan CryptoGenotyper Annotate with DGI Annotate with DGI HHsearch ABRicate Summary Glimmer ICM builder Glimmer3 Glimmer3 TB Variant Report TB Variant Filter lorikeet spoligotyping SpoTyping RepeatMasker scanMotifGenomeWide annotatePeaks findMotifsGenome Converts GTF to Annotations file for Homer SnpSift GeneSets List spaln parameter tables GECCO InterProScan TEfinder netboxr PlasmidFinder edta GffCompare PfamScan pharokka findMotifs 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 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

Multiple Alignments

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

Assembly

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

Mapping

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

Variant Calling

CNV VCF2JSON vcfanno BBTools: call variants plink SnpEff build: Strelka Germline sansa annotate Strelka Somatic Delly filter Delly merge Delly call Delly long-read (lr) bcftools consensus Delly classify Delly cnv JasmineSV Iris Variant Frequency Plot DCS mutations to tags/reads: SnpSift Filter DCS mutations to SSCS stats: Call specific mutations in reads: LUMPY LUMPY preprocessing Lofreq filter Call variants ARTIC minion cuteSV sniffles VarDict Control-FREEC GATK4 Mutect2 bcftools concat SnpEff eff: Realign reads Add LoFreq alignment quality scores Insert indel qualities seqwish odgi viz odgi build vg view vg deconstruct vg convert snippy-core snippy-clean_full_aln snippy bcftools merge VCFselectsamples: VCFannotateGenotypes: VCFdistance: VCFflatten: VCFcommonSamples: VCFannotate: VCF-VCFintersect: VCFbreakCreateMulti: VcfAllelicPrimitives: VCFgenotype-to-haplotype: VCFfilter: VCFfixup: VCFgenotypes: VCF-BEDintersect: VCFrandomSample: VCFhetHomAlleles: VCFsort: VCFprimers: VCFcombine: VCFleftAlign: VCFtoTab-delimited: VCFaddinfo: VCFcheck: bcftools call bcftools norm bcftools csq bcftools frameshifts bcftools color-chrs bcftools cnv SNP distance matrix Tag pileup frequency Finds SNP sites ExomeDepth FreeBayes VarScan somatic basil SnpSift Intervals SnpSift rmInfo SnpSift Variant Type SnpSift Annotate SnpSift CaseControl SnpEff chromosome-info: SnpSift Extract Fields SnpSift vcfCheck bcftoolsView BamLeftAlign VT normalize Naive Variant Caller (NVC) SnpEff databases: SnpSift GeneSets SnpSift dbNSFP SnpSift dbNSFP SnpEff download: SnpEff eff: Manta CNV Phenopacket DeepVariant VarScan copynumber VarScan VarScan mpileup SnpEff Ensembl CDS SnpEff to Peptide fasta bcftools split-vep Variant Annotator SnpSift Intervals SnpSift Annotate SnpSift Filter SnpSift CaseControl Get homopolymer run length 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 KING ARTIC guppyplex pharmCAT Predict variant effects breseq Convert VCF to MAF bcftools setGT bcftools setGT faToVcf CNVkit Access CNVkit Antitarget CNVkit Autobin CNVkit Batch CNVkit Call CNVkit Coverage CNVkit Diagram CNVkit Fix CNVkit Heatmap CNVkit Reference CNVkit Scatter CNVkit Segment CNVkit Target Frameshift Deletions Checks Beacon2 CSV2XLSX Beacon2 PXF2BFF Beacon2 VCF2BFF CNVkit Breaks CNVkit genemetrics CNVkit Segmetrics CNVkit Sex

Genome editing

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

RNA-Seq

blockbuster

RNA Analysis

CMsearch deoverlap RBPBench riboWaltz-plot Arriba 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 Arriba Draw Fusions Arriba Get Filters riboWaltz 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 GenomicSuperSignature barrnap CIRCexplorer2 CEMiTool Train a CheRRI model using RRIs miRNAture Evaluation of RRIs using CheRRI IsoformSwitchAnalyzeR Sleuth Trinity Stats PsiCLASS

Peak Calling

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

Epigenetics

hifive 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 cooler_makebins cooler csort with tabix cooler_cload_tabix cooler_balance Hicup to juicer converter

Phylogenetics

RAxML HyPhy-PRIME HyPhy-BUSTED HyPhy-BGM HyPhy-GARD HyPhy-aBSREL HyPhy-FUBAR HyPhy-FADE HyPhy-SM2019 HyPhy-MEME HyPhy-SLAC HyPhy-FEL T-Coffee HyPhy-RELAX UShER matUtils UShER sarscov2formatter GeneSeqToFamily preparation PhyML sarscov2summary Pangolin HybPiper Gene Copy Number Finder hcluster_sg parser ETE lineage generator ETE species tree generator ETE GeneTree splitter Homology Classifier and Filter ETE taxa DB generator ETE mod TreeBeST best Species tree generator Gene Align and Family Aggregator TreeBeST best FASTA header converter hcluster_sg BLAST parser NextAlign Nextclade HyPhy-Conv Annotate Replace ambiguous codons HyPhy-CFEL 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 Related Genomes Convert XMFA to percent identity table

Phenotype Association

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

Single-cell

Plot Filter Cluster, infer trajectories and embed SCEasy Converter baredSC 1d Normalize Inspect and manipulate Inspect AnnData Export AnnData and loom files Remove confounders Combine multiple 2D Models Combine multiple 1D Models Import Anndata and loom Manipulate AnnData Manipulate loom object DropletUtils DropletUtils Read10x DropletUtils emptyDrops Alevin MuSiC Deconvolution Slice Image 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 baredSC 2d velocyto CLI Cluster Inspection using RaceID Initial processing using RaceID Clustering using RaceID Lineage computation using StemID Lineage Branch Analysis using StemID 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

Spatial Omics

Perform segmentation of multiplexed tissue data BaSiC Illumination ASHLAR UNetCoreograph UnMicst s3segmenter MCQUANT

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Genomics Toolkits

Picard

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

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

NCBI Blast

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 Diamond view Diamond Diamond makedb Magic-BLAST: map large RNA or DNA sequences BLAST Reciprocal Best Hits (RBH) BLAST top hit descriptions BBTools: call variants

HiCExplorer

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

RAD-seq

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

GraphClust

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

MiModD

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

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Metagenomics

Metagenomic Analysis

BiG-SCAPE Phyloseq: plot ordination ampvis2 OTU network plot ampvis2 frequency plot Kraken taxonomic report Recentrifuge DAS Tool ampvis2 core community analysis Extract the marker sequences and metadata LotuS2 MaxBin2 Polypolish ampvis2 alpha diversity Krona pie chart Kraken-filter Kraken-translate SemiBin: Contig annotations Kleborate Kraken2 dada2: makeSequenceTable dada2: plotQualityProfile dada2: mergePairs dada2: assignTaxonomy and addSpecies dada2: sequence counts dada2: plotComplexity dada2: learnErrors dada2: dada dada2: removeBimeraDenovo dada2: filterAndTrim MetaEuk Easy Predict staramr LAST-train MT2MQ VSearch search LASTal dRep dereplicate dRep compare LASTdb LAST-split MAF-convert mash screen MetaGeneAnnotator mash sketch sixgill merge sixgill filter sixgill build sixgill makefasta SRST2 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 CAT add_names CAT summarise CAT prepare 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 Generate heatmap metagenomeSeq Normalization Convert Kraken Scoary jellyfish HUMAnN Perform metadata association Barplot Join (merge) Reduce Regroup Rename features Renormalize Normalize Split a HUMAnN table Split Make strain profiles Unpack pathway abundances MetaPhlAn Customize the marker sequences and metadata MetaBAT2 ampvis2 boxplot ampvis2 export fasta 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 samples ampvis2 subset data ampvis2 timeseries plot ampvis2 venn diagram SeqSero2 Bracken CoverM contig CoverM genome Converts genome bins in fasta format Create phyloseq object Create phyloseq object virAnnot Blast2tsv virAnnot OTU virAnnot Rps2tsv Phyloseq: plot alpha diverstiy measure Calculate contig depths SemiBin SemiBin: Group the contigs SemiBin: Concatenate fasta files SemiBin: Generate sequence features SemiBin: Train InStrain Profile InStrain Compare MaAsLin 2 MALT analyzer MEGAN: Generate a MEGAN rma6 file MEGAN: Generate RMA files MEGAN Blast2LCA: apply LCA alignment Binning refiner 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 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 Kraken-biom VAPOR 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 Combine MetaPhlAn and HUMAnN outputs MAPseq

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 templates for raster files Make templates for data tables Make templates Make EML EML to EAL Make geographic coverage template Make taxonomic coverage template Make templates for vector files Make entities templates for raster, vector and other entities files

Virology

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

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Proteomics, Metabolomics, Chemistry

Proteomics

XFDR PercolatorAdapter XMLValidator OpenSwathConfidenceScoring PeakPickerIterative OpenPepXL RNPxlXICFilter MassTraceExtractor ERPairFinder FileMerger FeatureFinderMRM ConsensusID SpectraFilterMarkerMower BaselineFilter TextExporter Proteinortho summary Proteinortho grab proteins Proteinortho DIA-NN PepQuery2 Show Sets PepQuery2 MaxQuant MSstatsTMT MSstats 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 MultiplexResolver PSM-Fragment Validator Remove protonation state OpenSwathFeatureXMLToTSV OpenSwathDIAPreScoring MapStatistics DigestorMotif FeatureLinkerLabeled XTandemAdapter SpectraFilterWindowMower OpenSwathWorkflow QCMerger IDMapper IDMassAccuracy IDRTCalibration IDSplitter MRMTransitionGroupPicker MapAlignerIdentification IsobaricAnalyzer ClusterMassTraces ClusterMassTracesByPrecursor CometAdapter CompNovo CompNovoCID IDMerger MetaboliteSpectralMatcher RTEvaluation QCExporter SpectraFilterNormalizer InternalCalibration Digestor PepNovoAdapter PeptideIndexer MapRTTransformer DTAExtractor OpenSwathAssayGenerator MetaProSIP SequenceCoverageCalculator ProteinQuantifier IDConflictResolver PeakPickerWavelet FuzzyDiff Decharger MzMLSplitter FileConverter SpectraFilterNLargest MassCalculator SpectraFilterThresholdMower MapAlignerPoseClustering QCEmbedder Epifany SpectraMerger PTModel OpenSwathDecoyGenerator ProteinInference TargetedFileConverter TOFCalibration TransformationEvaluation IDRipper SvmTheoreticalSpectrumGeneratorTrainer MascotAdapterOnline SpectraSTSearchAdapter SpectraFilterSqrtMower SemanticValidator SpecLibSearcher LabeledEval MapAlignerSpectrum SpecLibCreator MaRaClusterAdapter SimpleSearchEngine PrecursorIonSelector SeedListGenerator RTModel FeatureFinderCentroided RNPxlSearch SpectraFilterParentPeakMower TICCalculator IDFilter NucleicAcidSearchEngine MRMMapper OMSSAAdapter EICExtractor MyriMatchAdapter SpectraFilterBernNorm MSSimulator RNADigestor CVInspector MSI Qualitycontrol DecoyDatabase ExternalCalibration FalseDiscoveryRate FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMultiplex FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FFEval FidoAdapter FileFilter FileInfo GNPSExport AccurateMassSearch DatabaseFilter DeMeanderize FeatureFinderSuperHirn MSI classification OpenSwathMzMLFileCacher OpenSwathRewriteToFeatureXML IDPosteriorErrorProbability IDFileConverter MSI data exporter MSI segmentation MSI filtering IDScoreSwitcher MapAlignerTreeGuided 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 MaxQuant (using mqpar.xml) MT2MQ PepQuery MyriMatch idpEmbedder idpQonvert idpAssemble PepQuery2 index PyProphet export moFF Unipept MALDIquant peak detection PyProphet score Kronik Hardklor diapysef library generation PyProphet merge PyProphet peptide PyProphet protein PyProphet subsample 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 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 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 calisp eggNOG Mapper eggNOG Mapper

Metabolomics

matchms add key dimet timecourse analysis dimet pca analysis dimet metabologram dimet differential analysis matchms metadata match dimet bivariate analysis dimet pca plot dimet enrichment plot dimet abundance plot matchms subsetting matchms metadata export RECETOX MsFinder matchms filtering matchms scores formatter matchms metadata merge Transformation Anova Multivariate Biosigner Univariate MZMine batch Align Samples Replicate Filter Process Scans (and SIM-Stitch) MetFrag Vis Get peaklists Convert DIMSpy-based HDF5 to tsv Missing Values Sample Filter Sample Filter Blank Filter SIRIUS-CSI:FingerID 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 Heatmap genform NMR_Annotation xcms get a sampleMetadata file Table Merge Intensity Check ID choice Normalization mixmodel ASCA Between-table Correlation HMDB MS search bank_inhouse LCMS matching Golm Metabolome Database search spectrum NMR_Preprocessing NMR_Read xcms process history CAMERA.annotate xcms fillChromPeaks (fillPeaks) xcms adjustRtime (retcor) xcms groupChromPeaks (group) xcms findChromPeaks Merger xcms plot chromatogram xcms findChromPeaks (xcmsSet) MSnbase readMSData Lipidmaps OPLS-DA_Contrasts Join +/- Ions Generic_Filter Quality Metrics metaMS.runGC Multilevel Check Format Determine_batch_correction Batch_correction MassBank spectrum searches ProbMetab Tool CAMERA.combinexsAnnos proFIA NMR_Bucketing NMR_Normalization NMR spectra alignment NMR spectra alignment matchms convert matchms fingerprint similarity matchms networking matchms spectral similarity matchms remove key matchms split library dimet differential multigroup analysis dimet isotopologues plot RIAssigner use theoretical m/z values RIAssigner init from comment tracegroomer 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 RAMClustR RAMClustR define experiment recetox-xMSannotator matchms similarity WaveICA

ChemicalToolBox

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

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Statistics and Visualisation

Statistics

MINE Draw ROC plot Perform LDA Generate A Matrix Count GFF Features Correlation Perform Best-subsets Regression Principal Component Analysis Kernel Principal Component Analysis Sparse Matrix Functions Kernel Canonical Correlation Analysis Canonical Correlation Analysis T Test for Two Samples 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 Summary Statistics Count

Machine Learning

Random Forest model Prediction of Breast Cancer (BC) MCL Split Dataset Train, Test and Evaluation Principal component analysis Evaluate a Fitted Model Model Prediction Machine Learning Visualization Extension LightGBM Numeric Clustering Stacking Ensembles Deep learning training and evaluation Support vector machines (SVMs) 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 Fit a Pipeline, Ensemble 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 Label encoder To categorical Colorize label map virhunter decontaminator DeepMicro

Graph/Display Data

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

Muon Spectroscopy

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

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Miscellaneous Tools

Evolution

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

Motif Tools

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

Test Tools

ChIPpeakAnno annoPeaks Cluster Profiler Bitr Cluster Profiler GO 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 HE/ MALDI Image Registration NetCDF to Zarr JBrowse2

GIS Data Handling

OTB.MeanShiftSmoothing Run interpolation NetCDF xarray Metadata Info NetCDF xarray Selection OGR Informations OGR2ogr GDAL Warp GDAL Translate GDAL Merge GDAL Informations GDAL Build VRT GDAL addo OTB.BandMath NetCDF xarray operations NetCDF xarray map plotting NetCDF xarray Coordinate Info

Animal Detection on Acoustic Recordings

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

Compute indicators for satellite remote sensing

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

Regional Variation

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

Genome Diversity

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

Climate Analysis

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

Apollo

Register Account List Organisms 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

Convert point coordinates to binary image Convert label map to binary image Compute image orientation Perform gating Run generalist cell and nucleus segmentation FTP Link for Bioimage Archive Convert binary image to label map Perform curve fitting Perform affine image registration (intensity-based) Perform affine image registration (landmark-based) Compute image segmentation and object detection performance measures Perform color decomposition Overlay images Perform wavelet transformation on 3D-image stack Perform segmentation using region-based fitting of overlapping ellipses Download IDR/OMERO Evaluate segmentation Extract 2D features Scale image Convert binary image to EDM 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 Performs projective transformation Skeletonize Find edges Add shadow effect Enhance contrast Find maxima Perform segmentation using watershed transformation Apply raw transformation Operate on pixels Apply elastic transformation Run CellProfiler pipeline Compare elastic and raw deformation Compose a raw and an elastic transformation Analyze particles Create new image Add or remove noise Compose two raw transformations Align two images Smooth image Analyze skeleton Compare opposite elastic deformations Compare two raw deformations Convert elastic transformation to raw Convert to binary Sharpen Compose two elastic transformations Adjust threshold Adapt an elastic transformation Filter 2D image Compute image features Threshold image Convert image format Perform histogram equalization Perform segmentation using deformable shape models Apply anisotropic diffusion Performs projective transformation with/without labels Perform 2D spot detection Perform linking in time series (nearest neighbors) Switch axis coordinates Filter label map by rules Show image info Convert binary image to points (center of masses) Merge neighbors in label map Slice image Split label map using morphological operators Concatenate images or channels Convert point coordinates to label map Convert label map to points (center of masses) Permutate image axes Count objects in label map Convert binary image to points (point coordinates) Convert to OME-Zarr Wound healing scratch assay Run multi-modal single-cell visualization Analyze and visualize spatial multi-omics data Rename OME-TIFF channels Process single-cell intensities Compute Voronoi tessellation Apply a morphological operation Process images using arithmetic expressions Visualize detections Extract top view from whole-slide image Image Converter Local Threshold Split objects

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

Astronomy

Astronomical Archives (IVOA) astropy fits2bitmap astropy fits2csv astropy fitsinfo

Interactive tools

Interactive Source Notebooks Run Napari Run CellProfiler tadviewer QGIS QuPath ODV Ilastik metashrimps Interactive Hdfview tool Scoop3-Argo Interactive DIVAnd Notebooks Interactive BlobToolKit Pavian Interactive MGnify Notebook Interactive JupyTool and notebook GPU-enabled Interactive Jupyter Notebook for Machine Learning Interactive Climate Notebook Interactive Pangeo Notebook Interactive Pangeo Machine Learning Notebook 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 geoexplorer radiant EtherCalc VRM Editor SimText iSEE metashark NEAL GeneNoteBook Holoviz Copernicus Data Space Ecosystem Qiskit Jupyter notebook STAC catalog IDEAL Phyloseq

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 deblur denoise-16S qiime2 longitudinal first-differences 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 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-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

Metagenomic Analysis

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

GATK Tools

Count Covariates

Built-in Converters

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