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Protein Database Downloader EGA Download Client Get sequences by Ensembl ID Get gene tree by Ensembl ID Get features by Ensembl ID IEDB Faster Download and Extract Reads in FASTQ Download and Extract Reads in FASTA/Q 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 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 Upload File SEEK test UCSC Main UCSC Archaea EBI 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 ENA Upload tool cURL Send to cloud Send data to Export datasets Split file Collapse Collection Split file Unzip Extract element identifiers Column Join Unzip Collection Zip Collection Filter failed Filter empty Flatten Collection Merge Collections Relabel List Identifiers Filter List Sort Collection Tag elements from file Apply Rule to Collection Build List Extract Dataset Compose text parameter value Parse parameter value
Replace column Add line to file Text reformatting Histogram diff Add input name as column Merge Columns Compute Switch axis coordinates Replace Table Compute Column Regex Find And Replace Regex Find And Replace Join two files Query Tabular Join Replace Text Replace chromosome names SQLite to tabular Unique lines Filter Tabular Replace Text JQ cast Sort melt Base Coverage Search in textfiles Text transformation Unfold Subtract Complement PRINSEQ Cluster Rebase GFF3 features Remove columns Sort Column Order Unique Select first Concatenate datasets Multi-Join Select last Cut Create text file Sort a row tac Coverage Regex Replace Arithmetic Operations Merge Intersect Fetch closest non-overlapping feature Get flanks Subtract Whole Dataset Unique Add column 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 GffCompare Filter FASTA Column arrange XPath Sub-sample sequences files Filter sequences by ID find in reference Filter Sort Select Select Extract features Filter GFF data by attribute Filter GFF data by feature count Filter GTF data by attribute values_list Column Join Transpose Reverse Datamash Datamash Subtract Join two Datasets Compare two Datasets Group
Extract MAF blocks Stitch Gene blocks CrossMap Wig CrossMap GFF CrossMap VCF CrossMap BAM CrossMap BED Tabular-to-FASTA FASTA-to-Tabular Tabular to FASTQ Thermo msconvert mz to sqlite idpQuery bed to protein map Convert gffCompare annotated GTF to BED Map peptides to a bed file Convert GFA to FASTA Resize coordinate window gffread msms_extractor bax2bam Image Montage Image Converter Create InterMine Interchange idconvert msconvert Subset Peak List idconvert Convert GTF to BED12 twoBitToFa Convert BAM to ScIdx bigWigToBedGraph AXT to concatenated FASTA AXT to FASTA AXT to LAV BED-to-GFF GFF-to-BED LAV to BED MAF to BED MAF to Interval MAF to FASTA Wiggle-to-Interval SFF converter GTF-to-BEDGraph Wig/BedGraph-to-bigWig BED-to-bigBed Convert genome coordinates 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 fastp Collapse Filter sequences by length FASTA-to-Tabular Tabular to FASTQ Tabular-to-FASTA Clip Remove sequencing artifacts Exonerate Trimmomatic UMI-tools count UMI-tools extract Sickle seqtk_sample UMI-tools group UMI-tools whitelist FLASH Cutadapt seqtk_comp seqtk_mutfa seqtk_hety seqtk_cutN seqtk_mergefa seqtk_trimfq seqtk_fqchk seqtk_randbase seqtk_subseq seqtk_dropse seqtk_mergepe seqtk_seq seqtk_listhet mQC Fasta Statistics filtlong Draw nucleotides distribution chart Barcode Splitter Get crosslinked nucleotides faSplit Trim putative adapter sequence Create binary barcodes Extract barcodes Extract alignment ends Merge PCR duplicates Remove spurious Remove 3'-end nts Je-Clip Je-Demultiplex Je-MarkDuplicates Je-Demultiplex-Illu UMI-tools deduplicate FASTA Merge Files and Filter Unique Sequences Thread nucleotides onto a protein alignment (back-translation) Filter sequences by mapping Trim Galore! lighter fastq-join Split Fasta Split Fasta Convert Compute quality statistics Draw quality score boxplot FastQC FASTQE MultiQC Trimmomatic FASTQ Summary Statistics MultiQC QualiMap Counts QC Samtools view Reheader QualiMap BamQC Convert SAM Generate pileup QualiMap Multi-Sample BamQC Split Convert, Merge, Randomize Tag pileup frequency Samtools fixmate Samtools fastx Samtools merge Samtools markdup Samtools stats Samtools flagstat Samtools idxstats Filter SAM or BAM, output SAM or BAM Split BedCov Samtools depth Samtools sort samtools mpileup BAM filter Call and phase CalMD Slice RmDup Filter Pileup-to-Interval Merge BAM Files BamHash bedtools ExpandBed bedtools NucBed bedtools GroupByBed bedtools Intersect intervals bedtools OverlapBed bedtools GetFastaBed bedtools MaskFastaBed bedtools MergeBED bedtools Multiple Intersect bedtools SortBED bedtools BAM to BED bedtools ComplementBed bedtools WindowBed bedtools AnnotateBed bedtools JaccardBed bedtools TagBed bedtools ClosestBed bedtools SpacingBed bedtools Merge BedGraph files bedtools MakeWindowsBed bedtools Compute both the depth and breadth of coverage bedtools Genome Coverage bedtools MultiCovBed bedtools SubtractBed bedtools ClusterBed bedtools SlopBed bedtools FlankBed bedtools LinksBed bedtools BED12 to BED6 bedtools BED to BAM bedtools MapBed bedtools BED to IGV bedtools ShuffleBed bedtools ReldistBed bedtools RandomBed bedtools BEDPE to BAM bedtools FisherBed GffCompare bedtools Convert from BAM to FastQ Create a BedGraph of genome coverage Merge BedGraph files Create a histogram of genome coverage bcftools csq bcftools cnv bcftools consensus bcftools norm bcftools call snippy VarScan somatic VCFfilter: VarScan mpileup VarScan copynumber VCFselectsamples: VCFannotateGenotypes: VCFflatten: VCFcommonSamples: VCFannotate: VCF-VCFintersect: VCFbreakCreateMulti: VcfAllelicPrimitives: VCFgenotype-to-haplotype: VCFfixup: VCFgenotypes: VCF-BEDintersect: VCFrandomSample: VCFhetHomAlleles: VCFsort: VCFprimers: VCFcombine: VCFleftAlign: VCFtoTab-delimited: VCFaddinfo: VCFcheck: VarScan bcftoolsView FreeBayes VCFdistance: Naive Variant Caller (NVC) snippy-core ococo BamLeftAlign VCFdistance: Variant Annotator Merge Intersect VT normalize bcftools view BamLeftAlign Compare Annotate Slice VCF Subset FLAIR correct FLAIR collapse CoNvex medaka variant tool medaka variant pipeline medaka consensus tool medaka consensus pipeline NanoComporeDB NanoPlot ont_fast5_api: Multi to single ont_fast5_api: Single to multi ont_fast5_api: Compress ont_fast5_api: Subset Nanopolish polyA Nanopolish eventalign Nanopolish methylation Nanopolish variants SampComp NanopolishComp: FreqMethCalculate NanopolishComp: EventalignCollapse Porechop Extract time Show nucleotide Show quality Extract reads Extract FASTQ Read length statistics Plot signals Plot performance Generate histogram Collector’s curve Generate box-whisker Get longest read Extract nanopore events
Table to GFF3 Complement Cluster Base Coverage Profile Annotations Translate BED transcripts Concatenate Join Translate BED Sequences Filter BED on splice junctions Aggregate datapoints Extract Genomic DNA Gene length and GC content FragGeneScan 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
annotateMyIDs MOB-Recon MOB-Typer ectyper sistr_cmd CryptoGenotyper MITOS Busco RepeatMasker Antismash ChIPseeker Roary alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmscan hmmsearch jackhmmer nhmmer nhmmscan phmmer Convert XMFA to gapped GFF3 MLST List MLST Prokka Genbank to GFF3 ABRicate List ABRicate MITOS2 Exonerate seq2HLA FastANI Tn5Gaps Resampling HMM Gumbel Convert GFF3 TB-Profiler Profile TETyper Train Augustus Augustus fargene KOBAS Annotate KOBAS Identify gProfiler SNPense gProfiler Random gProfiler GOSt gProfiler Orth gProfiler Convert BlastXML to gapped GFF3 Maker socru goseq progressiveMauve Train SNAP Map annotation ids fgsea Fasta Statistics Filter with SortMeRNA Spaln: align cDNA or Protein to genome GOSlimmer GOEnrichment Genome annotation statistics Hammock - cluster peptides 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 ProbMetab Tool LC/MS matching Nucleosome Predictions miRanda DotKnot Blast2GO nhmmer hmmsearch hmmconvert hmmfetch jackhmmer alimask hmmscan nhmmscan hmmemit phmmer hmmalign hmmbuild Nucleotide subsequence search GotohScan Interproscan functional predictions of ORFs Glimmer3 Glimmer ICM builder Glimmer3 Annotate with DGI Annotate with DGI SnpSift GeneSets MAF Coverage Stats Mummer Delta-Filter Mummerplot DNAdiff Nucmer Kc-Align Show-Coords SINA Chromeister ClustalW Automated multiple sequence Select Sequences MSABOOT Hammock - cluster peptides Format cd-hit outputs CD-HIT-EST CD-HIT PROTEIN MUSCLE Compalignp MAFFT CD-HIT-EST CD-HIT PROTEIN Shasta Flye assembly Lordec NOVOplasty MEGAHIT IDBA-TRAN Shovill Racon Minia Quast miniasm ABySS Create assemblies with Unicycler IDBA-HYBRID IDBA-UD Canu assembler SPAdes VelvetOptimiser pilon WTDBG metaSPAdes DISCO rnaSPAdes Assemble with MIRA v3.4 Edena (assembling) Edena (overlapping) SOPRA with prebuilt contigs SSAKE CRISPR Recognition Tool detect CRISPR sequences velvetg velveth RNA STAR HISAT2 Parse blast XML output Bowtie2 Megablast Lastz paired reads LASTZ Map with Bowtie for Illumina RNA STARSolo Map with minimap2 Bismark Mapper Map with KMA STAR-Fusion Bismark Deduplicate Bismark Pretty Report Bismark Meth. Extractor segemehl Owler Mapper Bismark LASTZ_D Map with BWA Map with BWA-MEM TopHat Map with Bowtie for SOLiD Map with BFAST Map with PerM Re-align with SRMA Map with Mosaik Delly filter Delly call Variant Frequency Plot Delly merge DCS mutations to tags/reads: DCS mutations to SSCS stats: Call specific mutations in reads: LUMPY preprocessing LUMPY Delly long-read (lr) Realign reads Lofreq filter Call variants plink ARTIC minion cuteSV sniffles VarDict Control-FREEC GATK4 Mutect2 bcftools concat SnpEff eff: 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: VarScan somatic bcftools call bcftools consensus SnpEff chromosome-info: bcftools norm bcftools csq bcftools frameshifts bcftools color-chrs bcftools cnv SNP distance matrix Tag pileup frequency Finds SNP sites VarScan copynumber VarScan mpileup ExomeDepth FreeBayes BamLeftAlign SnpEff build: MiXCR Analyze TB Variant Filter TB Variant Report SnpEff databases: basil SnpSift Filter SnpEff download: SnpSift Intervals SnpSift rmInfo SnpSift Annotate SnpSift Variant Type SnpSift CaseControl SnpSift Extract Fields SnpSift vcfCheck SnpEff eff: SnpSift GeneSets SnpSift dbNSFP SnpSift dbNSFP SnpEff Ensembl CDS SnpEff to Peptide fasta Naive Variant Caller Variant Annotator SnpSift Intervals SnpSift Annotate SnpSift Filter SnpSift CaseControl CRISPR Studio MAGeCKs test MAGeCK mle MAGeCK GSEA MAGeCK count MAGeCK pathway blockbuster featureCounts RNA Structure Prediction MiGMAP rnaQUAST scPipe Seurat TEtranscripts TransDecoder Alevin Filter Combined Transcripts eXpress Cuffmerge Cufflinks Cuffdiff Cuffcompare ChiRA collapse ChiRA merge ChiRA map ChiRA qauntify ChiRA extract Trinotate footprint Cuffnorm cummeRbund htseq-count Salmon quant DESeq2 StringTie StringTie merge Differential expression analysis Filter low expression transcripts Compute contig Ex90N50 statistic and Ex90 transcript count Build expression matrix Align reads and estimate abundance Generate SuperTranscripts Trinity sRNAPipe GraphProt Visualize Slamdunk Alleyoop QualiMap Counts QC QualiMap RNA-Seq QC tximport maSigPro Filter with SortMeRNA Salmon quantmerge GLASSgo IntaRNA Kallisto pseudo Kallisto quant edgeR Cross-contamination Barcode Filter limma DEXSeq DEXSeq-Count plotDEXSeq Extract and cluster differentially expressed transcripts Remove Unwanted Variation 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 Plant small RNA target prediction tool 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 FEELnc 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 Cuffquant Sailfish 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 RPKM Count Tophat Fusion Post blockbuster Kinwalker antaRNA RNABOB Get RT Stop Counts Iterative Mapping Reactivity Calculation Extract CuffDiff MiRDeep2 Mapper MiRDeep2 Quantifier MiRDeep2 RSEM prepare reference RSEM calculate expression RSEM trinity fasta to gene map SICER MACS CCAT Genrich DiffBind MACS2 bdgcmp MACS2 bdgbroadcall MACS2 refinepeak MACS2 bdgdiff MACS2 bdgpeakcall MACS2 predictd MACS2 randsample MACS2 filterdup MACS2 callpeak PEAKachu zerone PureCLIP JAMM Piranha Piranha CLIP Peakcaller 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 bwameth MethylDackel Hicup Truncater Hicup Pipeline Hicup Filter Hicup Digester Hicup Deduplicator EpiCSeg - Chromatin segmentation Hicup Mapper Calling Merging Find differentially methylated region (DMR) Filtering Plotting Tiling Smooth data Correlation matrix HyPhy-SLAC HyPhy-SM2019 HyPhy-MEME HyPhy-FADE HyPhy-RELAX HyPhy-FUBAR HyPhy-aBSREL HyPhy-BGM HyPhy-BUSTED HyPhy-PRIME sarscov2formatter HyPhy-FEL HyPhy-GARD Phyogenetic reconstruction with RAxML GeneSeqToFamily preparation PhyML sarscov2summary 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 T-Coffee hcluster_sg BLAST parser VCF to pgSnp snpFreq FunDO HVIS Separate pgSnp alleles CTD aaChanges phyloP SIFT g:Profiler DAVID LD PASS GPASS BEAM LPS MasterVar to pgSnp Inspect AnnData Manipulate loom object Manipulate AnnData Export AnnData and loom files Import Anndata and loom Filter Inspect and manipulate Normalize Plot Remove confounders DropletUtils Slice Image Cluster, infer trajectories and embed Alevin Scanpy ParameterIterator Cluster Inspection using RaceID 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 Lineage Branch Analysis using StemID Lineage computation using StemID Clustering using RaceID Initial processing using RaceID
FastqToSam CollectBaseDistributionByCycle AddOrReplaceReadGroups MeanQualityByCycle RevertOriginalBaseQualitiesAndAddMateCigar CollectHsMetrics SortSam RevertSam FixMateInformation Collect Alignment Summary Metrics NormalizeFasta Downsample SAM/BAM MergeBamAlignment MarkDuplicatesWithMateCigar CleanSam ReplaceSamHeader MergeSamFiles MarkDuplicates ValidateSamFile QualityScoreDistribution CollectRnaSeqMetrics BedToIntervalList CollectWgsMetrics Picard Collect Sequencing Artifact Metrics ReorderSam CollectGcBiasMetrics FilterSamReads AddCommentsToBam SamToFastq EstimateLibraryComplexity CollectInsertSizeMetrics SAM/BAM Alignment Summary Metrics BAM Index Statistics Add or Replace Groups Estimate Library Complexity Insertion size metrics Paired Read Mate Fixer estimateReadFiltering bamCompare bamCoverage bamPEFragmentSize bigwigCompare plotHeatmap correctGCBias multiBamSummary plotPCA computeMatrix computeGCBias multiBigwigSummary plotProfile plotCorrelation plotCoverage plotFingerprint computeMatrixOperations alignmentsieve plotEnrichment Hicup Deduplicator GEMINI query GEMINI annotate GEMINI load GEMINI database info GEMINI pathways GEMINI windower GEMINI inheritance pattern GEMINI interactions GEMINI qc GEMINI set_somatic GEMINI roh GEMINI fusions GEMINI lof_sieve GEMINI actionable_mutations GEMINI amend GEMINI stats GEMINI gene_wise GEMINI burden pepwheel wordcount trimest pepwindow pepwindowall charge degapseq infoseq splitter skipseq needle patmatdb marscan water getorf lindna msbar oddcomp fuzztran tcode pepcoil helixturnhelix iep merger equicktandem newcpgseek extractseq dreg maskfeat newcpgreport codcmp dottup supermatcher nthseq primersearch cutseq tranalign fuzzpro cai custom noreturn dotpath etandem octanol sigcleave wobble wordmatch union megamerger preg prettyseq prettyplot einverted sixpack syco cpgreport pepstats palindrome hmoment twofeat digest extractfeat showfeat shuffleseq dotmatcher seqmatchall matcher revseq plotcon trimseq pasteseq est2genome diffseq vectorstrip polydot transeq isochore backtranseq compseq freak pepinfo checktrans antigenic banana dan epestfind maskseq geecee fuzznuc cpgplot notseq seqret plotorf cai btwisted newseq chaos pepnet textsearch chips garnier cusp descseq cirdna tmap sirna coderet biosed Kraken2 BLAST XML to tabular NCBI BLAST+ database info NCBI BLAST+ blastdbcmd entry(s) NCBI BLAST+ blastn NCBI BLAST+ blastp NCBI BLAST+ blastx NCBI BLAST+ convert2blastmask NCBI BLAST+ dustmasker NCBI BLAST+ makeblastdb NCBI BLAST+ makeprofiledb NCBI BLAST+ rpsblast NCBI BLAST+ rpstblastn NCBI BLAST+ segmasker NCBI BLAST+ tblastn NCBI BLAST+ tblastx Kraken-translate Kraken-filter Krona pie chart Kraken-report Kraken Diamond Diamond Diamond makedb Kraken-mpa-report BLAST Reciprocal Best Hits (RBH) Convert Kraken Kraken taxonomic report Sub-sample sequences files BLAST top hit descriptions scHicQualityControl chicPlotViewpoint chicDifferentialTest chicAggregateStatistic chicSignificantInteractions chicViewpoint hicPlotViewpoint hicPlotSVL hicPlotMatrix hicPlotDistVsCounts hicPlotAverageRegions hicPCA hicFindTADs hicValidateLocations hicMergeLoops hicDetectLoops hicCorrelate hicCompartmentalization hicCompareMatrices hicAverageRegions hicAggregateContacts hicCorrectMatrix hicNormalize hicTransform hicSumMatrices hicMergeMatrixBins hicConvertFormat hicAdjustMatrix hicBuildMatrix hicFindRestSite hicInfo hicQuickQC chicViewpointBackgroundModel chicQualityControl scHicCorrectMatrices scHicPlotConsensusMatrices scHicPlotClusterProfiles scHicNormalize scHicCreateBulkMatrix scHicMergeToSCool scHicMergeMatrixBins scHicInfo scHicDemultiplex scHicConsensusMatrices scHicClusterSVL scHicClusterMinHash scHicClusterCompartments scHicCluster scHicAdjustMatrix hicPlotTADs Stacks2: gstacks Stacks2: process shortreads BayeScan Stacks: assemble read pairs by locus Stacks: cstacks Stacks2: kmer filter Stacks2: clone filter Stacks2: tsv2bam Stacks2: reference map Stacks2: de novo map Stacks2: process radtags Stacks2: populations 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 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 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
OPLS-DA_Contrasts dada2: plotComplexity MetaEuk Easy Predict staramr LAST-train LASTal MT2MQ VSearch search LASTdb Join LAST-split MAF-convert dRep dereplicate dRep compare dada2: plotQualityProfile dada2: mergePairs dada2: sequence counts dada2: assignTaxonomy and addSpecies dada2: makeSequenceTable dada2: learnErrors dada2: removeBimeraDenovo dada2: dada dada2: filterAndTrim mash screen MetaGeneAnnotator mash sketch sixgill merge sixgill filter sixgill build sixgill makefasta CAT contigs CAT bins khmer: Abundance Distribution khmer: Count Median khmer: Sequence partition all-in-one khmer: Normalize By Median khmer: Abundance Distribution (all-in-one) khmer: Extract partitions khmer: Filter reads khmer: Filter reads CAT add_names CAT summarise CAT prepare MaxBin2 eggNOG Mapper Interproscan functional predictions of ORFs Group abundances PlasFlow Vegan Diversity Vegan Fisher Alpha Vegan Rarefaction VSearch sorting VSearch chimera detection VSearch clustering VSearch masking VSearch alignment VSearch dereplication VSearch shuffling Compare outputs of HUMAnN2 for several samples Combine MetaPhlAn2 and HUMAnN2 outputs Format MetaPhlAn2 VALET GDCWebApp Split stratified table Renormalize Create a genus level gene families file Normalize Regroup Barplot HUMAnN2 Split Make strain profiles Rename Reduce Unpack pathway abundances to show genes included Associate Salmonella Subtyping Nonpareil MetaPhlAn2 Format MetaPhlAn2 Merge Generate heatmap metagenomeSeq Normalization Summarize taxa 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 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 Make.contigs Get.label Shhh.seqs Reverse.seqs Make.lookup Get.oturep Parsimony Get.relabund Summary.seqs Chimera.bellerophon Merge.sfffiles Remove.groups Remove.lineage Degap.seqs Summary.qual Cluster.split Cluster Heatmap.sim Summary.single Phylotype Seq.error Chimera.ccode Get.communitytype Deunique.seqs Clearcut Cooccurrence Chimera.slayer Pre.cluster Lefse Get.otus Rarefaction.single Get.coremicrobiome Filter.shared unifrac.unweighted Indicator Get.dists Remove.rare Consensus.seqs Libshuff Remove.seqs Dist.shared Align.seqs Merge.groups Align.check Count.seqs Sens.spec Fastq.info Get.group Normalize.shared Pca Mantel Rarefaction.shared Bin.seqs Get.otulist Classify.otu Screen.seqs Make.biom Classify.seqs Make.shared Amova Get.seqs Trim.flows Primer.design Get.groups Homova List.seqs Chimera.vsearch Venn Corr.axes Collect.shared Chimera.pintail Split.abund Mimarks.attributes Anosim Sub.sample Merge.files Chop.seqs Sffinfo Remove.otulabels Remove.otus Get.sabund Chimera.check Make.sra Make.group Trim.seqs Count.groups Nmds Metastats Otu.association List.otulabels Get.otulabels Create.database Deunique.tree Merge.taxsummary Get.sharedseqs Biom.info Pairwise.seqs Merge.count unifrac.weighted Pcr.seqs Taxonomy-to-Krona Chimera.perseus Split.groups Classify.tree Make.fastq Pcoa Summary.shared Sort.seqs Get.mimarkspackage Remove.dists Cluster.fragments Make.lefse Chimera.uchime Cluster.classic Filter.seqs Make Design Otu.hierarchy Unique.seqs Rename.seqs Shhh.flows Tree.shared Summary.tax Parse.list Dist.seqs Phylo.diversity Classify.rf Get.rabund Heatmap.bin Get.lineage Hcluster Collect.single Filter sequences by length obitab obistat obisort obiconvert obiclean obiuniq obigrep obiannotate NGSfilter Illuminapairedend - Assembling pair-end reads ivar consensus ivar removereads ivar trim ivar getmasked ivar variants ivar filtervariants
MSI mz images MSI plot spectra MSI preprocessing PeakPickerIterative PeakPickerHiRes DeMeanderize MultiplexResolver RNPxlXICFilter RNAMassCalculator MapStatistics OpenSwathWorkflow AccurateMassSearch IDMapper IDMassAccuracy IDPosteriorErrorProbability IDRTCalibration FeatureLinkerLabeled XTandemAdapter LuciphorAdapter MapAlignerIdentification IsobaricAnalyzer SpectraFilterWindowMower ConsensusID ERPairFinder QCMerger AssayGeneratorMetabo ClusterMassTraces ClusterMassTracesByPrecursor CometAdapter CompNovo MRMTransitionGroupPicker NovorAdapter IDMerger MetaboliteSpectralMatcher RTEvaluation QCExporter IDSplitter SpectraFilterNormalizer InternalCalibration MassTraceExtractor Digestor PeptideIndexer MapRTTransformer DTAExtractor MetaProSIP ProteinQuantifier FuzzyDiff MzMLSplitter PSMFeatureExtractor SpectraFilterNLargest SpectraFilterThresholdMower CompNovoCID SpectraMerger PTModel ProteinInference IDRipper MSGFPlusAdapter MascotAdapterOnline MassCalculator SemanticValidator MapAlignerPoseClustering QCEmbedder Epifany LabeledEval MaRaClusterAdapter OpenSwathDecoyGenerator PrecursorIonSelector TargetedFileConverter TextExporter TOFCalibration TransformationEvaluation FeatureFinderCentroided XMLValidator FeatureFinderSuperHirn SvmTheoreticalSpectrumGeneratorTrainer PepNovoAdapter SpectraSTSearchAdapter SpectraFilterSqrtMower SpectraFilterParentPeakMower SpectraFilterMarkerMower TICCalculator SpecLibSearcher OpenSwathAssayGenerator SpecLibCreator IDFilter SimpleSearchEngine SequenceCoverageCalculator SeedListGenerator SiriusAdapter MapAlignerSpectrum RTModel NucleicAcidSearchEngine RNPxlSearch IDConflictResolver PeakPickerWavelet SpectraFilterBernNorm MSFraggerAdapter MRMMapper OMSSAAdapter EICExtractor MyriMatchAdapter RNADigestor MSSimulator Decharger BaselineFilter FileConverter DatabaseFilter CVInspector PSM-Fragment Validator DecoyDatabase QualityControl MT2MQ Remove protonation state ExternalCalibration FalseDiscoveryRate FeatureFinderIdentification idpQuery OpenSwathConfidenceScoring FeatureFinderIsotopeWavelet FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMRM QCExtractor FeatureFinderMultiplex FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FFEval FidoAdapter FileFilter FileInfo FileMerger QCImporter GNPSExport ConsensusMapNormalizer IDFileConverter MetaboliteAdductDecharger IDScoreSwitcher QCCalculator PhosphoScoring MapAlignerTreeGuided OpenSwathRTNormalizer MapNormalizer OpenSwathFeatureXMLToTSV MascotAdapter MRMPairFinder OpenSwathMzMLFileCacher MSstatsConverter MzTabExporter OpenSwathDIAPreScoring NoiseFilterGaussian NoiseFilterSGolay OpenSwathAnalyzer OpenPepXLLF OpenSwathChromatogramExtractor OpenSwathFileSplitter OpenSwathRewriteToFeatureXML HighResPrecursorMassCorrector PrecursorMassCorrector LowMemPeakPickerHiResRandomAccess CruxAdapter SpectraFilterScaler ProteinResolver QCShrinker DigestorMotif LowMemPeakPickerHiRes MSI Qualitycontrol metaQuantome: stat metaQuantome: create samples file metaQuantome: visualize metaQuantome: filter metaQuantome: database MSI combine metaQuantome: expand MSI classification MSI segmentation MSI data exporter MSI filtering ConvertFastaToPrositCSV EncyclopeDIA Walnut EncyclopeDIA Quantify SearchToLib ConvertPrositCSVToLibrary ConvertLibraryToBlib IDExtractor eggNOG Mapper PepQuery MSstats MyriMatch idpEmbedder idpQonvert idpAssemble MaxQuant PyProphet export moFF Unipept MALDIquant peak detection PyProphet score MaxQuant (using mqpar.xml) Kronik Hardklor diapysef library generation PyProphet merge PyProphet peptide PyProphet protein PyProphet subsample Proteinortho summary Proteinortho grab proteins Proteinortho FlashLFQ QuantWiz-IQ Peptide Genomic Coodinate 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 MSI filtering MS-GF+ Protease prediction Calculate protein properties RTPredict OpenPepXL PTPredict InspectAdapter InclusionExclusionListCreator LowMemPeakPickerHiResRandomAccess IDDecoyProbability RNPxl XFDR PercolatorAdapter AdditiveSeries TopPerc Protease prediction Create Decoy Database (reverse) Morpheus X!Tandem MSMS Search X!Tandem MSMS Search Get peaklists Merge peaklists Convert DIMSpy-based HDF5 to tsv Missing Values Sample Filter Sample Filter Blank Filter Align Samples Replicate Filter Process Scans (and SIM-Stitch) SIRIUS-CSI:FingerID MetFrag msPurity.spectralMatching msPurity.purityX msPurity.dimsPredictPuritySingle 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 Add hydrogen atoms GROMACS structure configuration Create GROMACS index files Create GROMACS position restraints files APoc Extract energy components with GROMACS Modify/convert GROMACS trajectories GROMACS simulation GROMACS solvation and adding ions GROMACS energy minimization GROMACS initial setup Prepare ligands for docking Substructure Search Remove counterions and fragments Spectrophores search Change title Compute physico-chemical properties Remove protonation state Ramachandran Analysis End-to-End Analysis Cosine Content Hydrogen Bond Analysis Ramachandran Plots Distance Analysis Dihedral Analysis RDF Analysis Angle Analysis Remove duplicated molecules Filter Compound conversion Visualisation Compound search Remove small molecules Determine distance to defined points Hierarchical clustering Extract RMSD distance matrix data Extract clusters of MD trajectories ChEMBL structure pipeline dcTMD friction correction smina Prepare receptor Enumerate changes Extract values from an SD-file fpocket Search ChEMBL database Calculate molecular descriptors PubChem Download PubChem Assay Downloader VINA Docking Prepare ligand Calculate the box parameters using RDKit Descriptors Drug-likeness Score docked poses using SuCOS Cluster ligands using SuCOS Max SuCOS score Create Frankenstein ligand rDock cavity definition rDock docking rDock docking rxDock cavity definition rxDock docking SDF sort and filter Calculate plane of best fit for molecules Reaction SMARTS filter Generate conformers Constrained conformer generation Butina Cluster Matrix Open 3D Align Standardize SD-files Butina Cluster Pick Reaction maker Screen XCos 'FeatureStein' fragment overlay scoring Merge GROMACS topologies OpenDUck chunk Run OpenDUck XChem TransFS pose scoring Convert Parameters mmpbsa mmgbsa Molecule to fingerprint NxN clustering Taylor-Butina clustering SDF to Fingerprint MDTraj file converter ParmChk2 AnteChamber Generate MD topologies for small molecules fastpca Alchemical Analysis goseq 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 GROMACS NVT equilibration GROMACS production simulation GROMACS NPT equilibration 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
Sparse Matrix Functions 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 Create a model to recommend tools Wavelet variance GraphEmbed Landmark Registration Plot actual vs predicted curves and residual plots Plot confusion matrix, precision, recall and ROC and AUC curves Rolling window Nearest Neighbors Classification Support vector machines (SVMs) Anova Multivariate Univariate IWTomics Plot with Threshold IWTomics Test IWTomics Load Sequence composition Biosigner Transformation Heatmap Statistical hypothesis testing Summary Statistics Count Model Prediction Support vector machines (SVMs) Generate Estimator attributes Stacking Ensembles Hyperparameter Search Pipeline Builder Evaluate pairwise distances Nearest Neighbors Classification Numeric Clustering Ensemble methods Feature Selection Preprocess Calculate metrics Calculate metrics Discriminant Analysis Generalized linear models Model Validation Split Dataset Train, Test and Evaluation LightGBM Principal component analysis Build Deep learning Batch Training Models Create deep learning model Create a deep learning model architecture Evaluate a Fitted Model Fit a Pipeline, Ensemble Machine Learning Visualization Extension Deep learning training and evaluation Sparse Matrix Functions Create a model to recommend tools Violin plot w ggplot2 pyGenomeTracks Build custom track Scatterplot Histogram GMAJ Plotting tool JBrowse - Data Directory to Standalone JBrowse Circos: Interval to Tiles Circos: Resample 1/2D data Circos: Link Density Track Circos: bigWig to Scatter Circos: Interval to Circos Text Labels Circos: Alignments to links Circos: Table viewer Circos GC Skew Circos: Stack bigWigs as Histogram Circos: Bundle Links Scatterplot with ggplot2 Plot confusion matrix, precision, recall and ROC and AUC curves Newick Display Bandage Info Bandage Image UpSet diagram Pairwise intersection Krona pie chart Pathview Export to GraPhlAn Venn Diagram Volcano Plot heatmap2 Plot actual vs predicted curves and residual plots Parallel Coordinates Plot Histogram w ggplot2 Heatmap w ggplot 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 Bar chart Boxplot LAJ VCF to MAF Custom Track
Mutate Codons IQ-TREE codeML Structure aaChanges phyloP Sequence Logo MEME psp-gen FIMO MEME MEME-ChIP DREME ChIPpeakAnno annoPeaks Cluster Profiler Bitr Cluster Profiler GO hifive PyIron Tombo Re-squiggle Tombo create Tombo detect modifications Tombo plot most signficant Tombo plot genome locations Peptide Prophet Protein Prophet InterProphet RaceID Discriminant Analysis Convert Transform Nearest Neighbors Classification Numeric Clustering Support vector machines (SVMs) Sparse Matrix Functions Preprocess Evaluate pairwise distances Generate Generalized linear models Ensemble methods Calculate metrics Protease prediction bwtool-lift Calculate protein properties Base Count Codon count GenBank and EBML Extract sequences from GenBank GFF converter Sequence converter Translate nucleotides RNALfoldz HE/ MALDI Image Registration OGR Informations OGR2ogr GDAL Warp GDAL Translate GDAL Merge GDAL Informations GDAL Build VRT GDAL addo Get species occurrences data Advanced restitution: 'Point fixe' protocol Advanced restitution: 'Routier'or 'Pedestre' protocols Tadarida data cleaner Tadarida identifications validation Fetch Indels Draw Stacked Bar Plots Delete Overlapping Indels Compute Motif Frequencies Compute Motif Frequencies For All Motifs Categorize Elements Feature coverage 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 Phyogenetic reconstruction with RAxML Aggregate Individuals 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 CTSM/FATES-EMERALD climate stripes map plot Copernicus Essential Climate Variables zonal statistics shift longitudes Delete all annotations from an Apollo record List Organisms Register Account Delete an Apollo record Create or Update Organism Annotate Retrieve Data GFF3 to Apollo Annotations Retrieve JBrowse SpyBOAT Operate on pixels IDR/OMERO Download Apply elastic transformation Watershed segmentation Apply raw transformation Find maxima Enhance contrast Find edges Add shadow effect Skeletonize Convert binary image to EDM Projective Transformation CellProfiler ImageMath SaveImages RelateObjects MeasureTexture MeasureObjectSizeShape MeasureObjectIntensity MeasureImageQuality MeasureImageIntensity MeasureImageAreaOccupied MeasureGranularity MaskImage IdentifyPrimaryObjects GrayToColor ExportToSpreadsheet EnhanceOrSuppressFeatures DisplayDataOnImage ConvertObjectsToImage Starting Modules Overlay Extract top view GeneSeqToFamily preparation Image Converter Landmark Registration Adapt an elastic transformation Adjust threshold Compose two elastic transformations Sharpen Convert to binary Convert elastic transformation to raw Compare two raw deformations Compare opposite elastic deformations Analyze skeleton Smooth Align two images Compose two raw transformations Add or remove noise Create new image Analyze particles Compose a raw and an elastic transformation Compare elastic and raw deformation Image Info Detection Visualization Local Threshold Auto Threshold Histogram equalization Convert image Colocalization 2D Feature Extraction Permutate image Label to Points Points to Label Concatenate images Scale Image Merge Neighbours in Label Binary 2 Label Filter segmentation Split objects Anisotropic Diffusion Color Deconvolution Filter Image Points to Label Switch axis coordinates Coordinates of ROI Count Objects Mahotas-features Overlay Segmentation Mask Points to Binary Image Projective Transformation Visceral Binary To Points Slice Image Split Labelmap Compute GLM on population data Compute GLM on community data Calculate presence absence table Calculate community metrics Create a plot from GLM data Temporal trend indicator Estimate temporal population evolution Estimate temporal population evolution Filter species Model temporal trend Flight curve Autocorrelation test Expected temporal trend Linear regression ajusted Plot abundance Abundance index Interactive Jupyter Notebook Interactive Climate Notebook RStudio PyIron Interactive Jupyter Notebook HiGlass OpenRefine Ubuntu XFCE Desktop Panoply AskOmics Interactive CellXgene Environment 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 Scanpy ScaleData Scanpy RunUMAP Scanpy FindMarkers Scanpy ParameterIterator Scanpy PlotTrajectory Scmap index cells 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 EBI SCXA Data Retrieval Filter pileup Convert SAM Merge BAM Files Generate pileup flagstat MPileup rmdup Slice BAM Pileup-to-Interval Summarize taxonomy Draw phylogeny Poisson two-sample test Find lowest diagnostic rank Fetch taxonomic representation Find diagnostic hits Count Covariates