| layout |
|---|
default |
NCBI Datasets Genomes EGA Download Client IEDB Protein Database Downloader NCBI Datasets Genomes Faster Download and Extract Reads in FASTQ Download and Extract Reads in BAM NCBI Accession Download Download and Generate Pileup Format UniProt Get species occurrences data Unipept NCBI ESearch NCBI EGQuery NCBI ECitMatch NCBI EPost NCBI ELink NCBI EInfo NCBI ESummary NCBI EFetch UniProt Get sequences by Ensembl ID Get gene tree by Ensembl ID Get features by Ensembl ID Search ENA data Retrieve ENA data Retrieve ENA taxon data Retrieve an analysis report Retrieve a run report EBI Search DoRiNA Search Download run data Upload File SEEK test UCSC Main UCSC Archaea 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 to cloud ENA Upload tool cURL Export datasets Export datasets Split file Split file Collapse Collection 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 Compose text parameter value Calculate numeric parameter value Parse parameter value
Histogram Compute diff Replace column Add line to file Add input name as column Merge Columns Switch axis coordinates Table Compute Column Regex Find And Replace Regex Find And Replace Join two files Replace Query Tabular Replace chromosome names SQLite to tabular Replace Text Filter Tabular JQ cast Replace Text melt Base Coverage Subtract Text reformatting PRINSEQ Cluster Rebase GFF3 features Remove columns Sort Column Order Join tac Concatenate datasets Multi-Join Unique lines Advanced Cut Select last Sort a row Sort Search in textfiles Unfold Text transformation Create text file Select first Unique Coverage Regex Replace Arithmetic Operations Merge Intersect Fetch closest non-overlapping feature Get flanks Complement Subtract Whole Dataset Unique Add column 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 a 10X BAM file to FASTQ BED-to-GFF GFF-to-BED MAF to BED MAF to Interval MAF to FASTA SFF converter Wig/BedGraph-to-bigWig BED-to-bigBed 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 Reverse Datamash Column join Transpose Datamash Subtract Join two Datasets Compare two Datasets Group
xmlstarlet Convert Tabular-to-FASTA FASTA-to-Tabular Tabular to FASTQ GFA to FASTA Thermo msconvert Extract MAF blocks CrossMap Wig CrossMap VCF CrossMap GFF CrossMap BED Stitch Gene blocks CrossMap BAM mz to sqlite idpQuery bed to protein map Convert gffCompare annotated GTF to BED Map peptides to a bed file Resize coordinate window gffread msms_extractor bax2bam Image Montage Image Converter Create InterMine Interchange idconvert msconvert Subset Peak List idconvert Convert GTF to BED12 twoBitToFa Convert BAM to ScIdx bigWigToBedGraph Convert BAM CrossMap region samtools BAM to CRAM ab1 to FASTQ converter Compress file(s) 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 Trimmomatic Collapse FASTQE fastp Filter sequences by length FASTA-to-Tabular Cutadapt Tabular to FASTQ Tabular-to-FASTA Remove sequencing artifacts Exonerate FastQC Trim Galore! UMI-tools count UMI-tools extract Sickle seqtk_sample UMI-tools group UMI-tools whitelist FLASH seqtk_comp seqtk_mutfa seqtk_hety seqtk_cutN seqtk_mergefa seqtk_trimfq seqtk_fqchk seqtk_randbase seqtk_subseq seqtk_dropse seqtk_mergepe seqtk_seq seqtk_listhet mQC Fasta Statistics filtlong Clip Draw nucleotides distribution chart Barcode Splitter Get crosslinked nucleotides faSplit Trim putative adapter sequence Create binary barcodes Extract barcodes Extract alignment ends Merge PCR duplicates Remove spurious Remove 3'-end nts Je-Clip Je-Demultiplex Je-MarkDuplicates Je-Demultiplex-Illu UMI-tools deduplicate FASTA Merge Files and Filter Unique Sequences Thread nucleotides onto a protein alignment (back-translation) Filter sequences by mapping lighter fastq-join Split Fasta RNA-seq Rcorrector Pear Pear Convert Compute quality statistics Draw quality score boxplot MultiQC QualiMap Counts QC FASTQ info Samtools view Pileup-to-Interval Samtools reheader QualiMap BamQC Convert SAM Generate pileup QualiMap Multi-Sample BamQC Split Convert, Merge, Randomize Tag pileup frequency Samtools markdup Samtools merge Samtools fastx Samtools fixmate Samtools stats Samtools flagstat Samtools idxstats Filter SAM or BAM, output SAM or BAM Samtools split Samtools bedcov Samtools depth Samtools sort Samtools coverage Samtools mpileup BAM filter Samtools phase Samtools calmd Slice RmDup Filter Merge BAM Files BamHash Split BAM by Paired/Single End Split BAM by Reference Split BAM by Mapped Split BAM by Tag VarScan mpileup VarScan Somatic VarScan Somatic BamUtil diff bedtools ExpandBed bedtools NucBed bedtools GroupByBed bedtools Intersect intervals bedtools OverlapBed bedtools getfasta bedtools MaskFastaBed bedtools MergeBED bedtools Multiple Intersect bedtools SortBED bedtools BAM to BED bedtools ComplementBed bedtools WindowBed bedtools AnnotateBed bedtools JaccardBed bedtools TagBed bedtools ClosestBed bedtools SpacingBed bedtools Merge BedGraph files bedtools MakeWindowsBed bedtools Compute both the depth and breadth of coverage bedtools Genome Coverage bedtools MultiCovBed bedtools SubtractBed bedtools ClusterBed bedtools SlopBed bedtools FlankBed bedtools LinksBed bedtools BED12 to BED6 bedtools BED to BAM bedtools MapBed bedtools BED to IGV bedtools ShuffleBed bedtools ReldistBed bedtools RandomBed bedtools BEDPE to BAM bedtools FisherBed GffCompare bedtools Convert from BAM to FastQ Create a BedGraph of genome coverage Merge BedGraph files Create a histogram of genome coverage bcftools csq bcftools cnv bcftools consensus bcftools norm bcftools call VarScan somatic VCFfilter: VCFselectsamples: VCFannotateGenotypes: VCFflatten: VCFcommonSamples: vcfanno VCFannotate: VCF-VCFintersect: VCFbreakCreateMulti: VcfAllelicPrimitives: VCFgenotype-to-haplotype: VCFfixup: VCFgenotypes: VCF-BEDintersect: VCFrandomSample: VCFhetHomAlleles: VCFsort: VCFprimers: VCFcombine: VCFleftAlign: VCFtoTab-delimited: VCFaddinfo: VCFcheck: VarScan VarScan copynumber VarScan mpileup bcftoolsView FreeBayes VCFdistance: Naive Variant Caller (NVC) snippy snippy-core ococo BamLeftAlign VCFdistance: Variant Annotator Merge Intersect VT normalize VCFdistance: VCFbreakCreateMulti: VCFtoTab-delimited: VCFgenotype-to-haplotype: VCFaddinfo: VcfAllelicPrimitives: VCFannotate: VCFannotateGenotypes: VCF-BEDintersect: VCFgenotypes: VCFcheck: VCFcombine: VCFcommonSamples: Compare Annotate Slice VCF Subset 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 polyA Nanopolish eventalign Nanopolish methylation Nanopolish variants SampComp NanopolishComp: FreqMethCalculate NanopolishComp: EventalignCollapse Porechop Extract time Show nucleotide Show quality Extract reads Extract FASTQ Read length statistics Plot signals Plot performance Generate histogram Collector’s curve Generate box-whisker Get longest read Extract nanopore events Pycoqc
Complement Cluster Base Coverage Profile Annotations Table to GFF3 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
InterProScan Busco OptiType Prokka Roary TB-Profiler Profile nhmmer hmmbuild hmmscan phmmer jackhmmer nhmmscan hmmsearch KofamScan Table to GFF3 annotateMyIDs MOB-Recon MOB-Typer ectyper sistr_cmd MITOS Antismash ChIPseeker progressiveMauve Convert XMFA to gapped GFF3 MLST List MLST Genbank to GFF3 MITOS2 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 Train SNAP Map annotation ids fgsea Filter with SortMeRNA prot-scriber 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 nhmmscan hmmemit phmmer hmmalign hmmbuild alimask hmmalign hmmconvert hmmemit hmmfetch Nucleotide subsequence search GotohScan CryptoGenotyper Interproscan functional predictions of ORFs Annotate with DGI Annotate with DGI HHsearch ABRicate Summary Glimmer ICM builder Glimmer3 Glimmer3 TB Variant Report TB Variant Filter lorikeet spoligotyping SpoTyping RepeatModeler RepeatMasker scanMotifGenomeWide annotatePeaks findMotifsGenome Converts GTF to Annotations file for Homer SnpSift GeneSets hamronize summarize OrthoFinder Funannotate assembly clean Sort assembly Funannotate predict annotation Funannotate compare Funannotate functional List spaln parameter tables GECCO legsta ClustalW SINA Gecko Chromeister MAF Coverage Stats Mummer Mummerplot MAFFT add MAFFT Delta-Filter Nucmer DNAdiff Show-Coords Kc-Align Automated multiple sequence Select Sequences MSABOOT Hammock - cluster peptides Format cd-hit outputs MUSCLE Compalignp cd-hit SPAdes Merqury gfastats Racon Hifiasm Trycycler cluster Trycycler consensus Trycycler partition Trycycler reconcile/msa Trycycler subsample Canu assembler MITObim TrimN Purge overlaps AEGeAn ParsEval AEGeAn LocusPocus AEGeAn GAEVAL AEGeAn CanonGFF3 SALSA Shasta Lordec NOVOplasty MEGAHIT IDBA-TRAN Shovill Minia Flye Quast miniasm ABySS Create assemblies with Unicycler IDBA-UD IDBA-HYBRID VelvetOptimiser pilon WTDBG metaSPAdes DISCO rnaSPAdes Meryl Assemble with MIRA v3.4 Edena (assembling) Edena (overlapping) SOPRA with prebuilt contigs SSAKE CRISPR Recognition Tool detect CRISPR sequences GenomeScope PretextMap Bionano Hybrid Scaffold Filter and merge MitoHiFi Raven RagTag TGS-GapCloser HyPo rnaviralSPAdes plasmidSPAdes metaviralSPAdes metaplasmidSPAdes coronaSPAdes biosyntheticSPAdes LINKS velvetg velveth Parse blast XML output Megablast Lastz paired reads LASTZ Map with Bowtie for Illumina Map with minimap2 HISAT2 RNA STARSolo RNA STAR Bismark Mapper Map with KMA STAR-Fusion Bismark Deduplicate Bismark Pretty Report Bismark Meth. Extractor Bowtie2 segemehl Owler Mapper Bismark Map with BWA Map with BWA-MEM LASTZ_D TopHat Map with Bowtie for SOLiD Winnowmap Align sequences BWA-MEM2 Map with BFAST BBTools: BBMap Map with PerM Re-align with SRMA Map with Mosaik pharmCAT seqwish Strelka Germline sansa annotate Strelka Somatic Delly filter Delly merge Delly call Delly long-read (lr) bcftools consensus Delly classify Delly cnv vcfanno JasmineSV Iris Variant Frequency Plot DCS mutations to tags/reads: SnpSift Filter DCS mutations to SSCS stats: Call specific mutations in reads: LUMPY LUMPY preprocessing Lofreq filter Call variants plink ARTIC minion cuteSV sniffles VarDict Control-FREEC GATK4 Mutect2 bcftools concat SnpEff eff: Realign reads Add LoFreq alignment quality scores Insert indel qualities odgi viz odgi build vg view vg deconstruct vg convert snippy-core snippy-clean_full_aln snippy KING 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 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 ExomeDepth FreeBayes SnpEff build: MiXCR Analyze TB Variant Filter TB Variant Report SnpEff databases: basil 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 BamLeftAlign SnpEff Ensembl CDS SnpEff to Peptide fasta Naive Variant Caller 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 DeepVariant ARTIC guppyplex VarScan mpileup BBTools: call variants CRISPR Studio MAGeCKs test MAGeCK mle MAGeCK GSEA MAGeCK count MAGeCK pathway parse mykrobe predict AmpliCan blockbuster Seurat Filter Combined Transcripts plotDEXSeq eXpress Cuffmerge Cufflinks Cuffdiff Cuffcompare rnaQUAST Remove Unwanted Variation FEELnc featureCounts MiGMAP scPipe TEtranscripts TransDecoder ChiRA collapse ChiRA merge ChiRA map ChiRA qauntify ChiRA extract Trinotate footprint Cuffnorm cummeRbund htseq-count Salmon quant DESeq2 StringTie StringTie merge Align reads and estimate abundance Trinity sRNAPipe GraphProt Visualize Slamdunk Alleyoop QualiMap Counts QC QualiMap RNA-Seq QC tximport maSigPro Generate SuperTranscripts Build expression matrix Compute contig Ex90N50 statistic and Ex90 transcript count Filter low expression transcripts Differential expression analysis Filter with SortMeRNA Salmon quantmerge GLASSgo IntaRNA Kallisto pseudo Kallisto quant edgeR Cross-contamination Barcode Filter limma DEXSeq DEXSeq-Count Extract and cluster differentially expressed transcripts EGSEA Select Sequences Cofold RNAz Cluster Dr. Disco (classify) Dr. Disco (fix) Dr. Disco (bam-extract) Dr. Disco (integrate) Dr. Disco (detect) MEA CMCV RNAz Randomize Aln RNAz Select Seqs RNAz windows Annotate RNAz Annotate DESeq2/DEXSeq output tables LocARNA Multiple Aligner cmv ribotaper part 2: metagene analysis for P-sites definition ribotaper part 3: ribosome profiling ribotaper part 1: creation of annotation files PIPmiR PIPELINE NASTIseq FlaiMapper TargetFinder Get motifs from AREsite2 FuMa RNAlien BlockClust Generate gene to transcript map RNASeq samples quality check Describe samples Partition genes into expression clusters Gene Body Coverage (BAM) Fit a BUM model Identify optimal scoring subnetwork Calculate a Heinz score ssHMM pizzly RCAS Gene Body Coverage (Bigwig) RPKM Saturation Infer Experiment RNA fragment size Transcript Integrity Number Junction Saturation FPKM Count Read Distribution RNAcode Junction Annotation Inner Distance RNAz RNAshapes RNAfold IDR RNAcofold RNAalifold Deletion Profile Read NVC BAM/SAM Mapping Stats Read Duplication Read GC Insertion Profile BAM to Wiggle Clipping Profile Read Quality Hexamer frequency Mismatch Profile segemehl Sailfish Cuffquant RNAeval RNAplex RNA2Dfold RNApaln RNAplot RNAsnoop Kinfold RNAaliduplex RNAduplex RNAdistance RNApdist RNALfold RNAPKplex RNAup RNALalifold RNAinverse RNAheat RNAsubopt cmalign cmsearch cmscan cmpress cmbuild cmstat remuRNA RNAsnp LocARNA PARalyzer CIRCexplorer RNAcommender RPKM Count 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 MACS SICER CCAT Genrich DiffBind MACS2 bdgcmp MACS2 bdgbroadcall MACS2 refinepeak MACS2 bdgdiff MACS2 bdgpeakcall MACS2 predictd MACS2 randsample MACS2 filterdup MACS2 callpeak PEAKachu zerone PureCLIP 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 Pangolin 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 sarscov2formatter 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 hcluster_sg BLAST parser NextAlign Nextclade HyPhy-Conv Annotate Replace ambiguous codons HyPhy-CFEL UShER matUtils UShER HyPhy-Summary SNP distance matrix VCF to pgSnp snpFreq FunDO HVIS Separate pgSnp alleles CTD aaChanges phyloP SIFT g:Profiler DAVID LD PASS GPASS BEAM LPS MasterVar to pgSnp Manipulate loom object MuSiC Deconvolution Manipulate Expression Set Object MuSiC Compare Import Anndata and loom Export AnnData and loom files Manipulate AnnData Inspect AnnData DropletUtils DropletUtils Read10x DropletUtils emptyDrops Alevin Filter Inspect and manipulate Normalize Plot Remove confounders Slice Image Cluster, infer trajectories and embed Inspect Expression Set Object Construct Expression Set Object Scanpy ParameterIterator Scater: t-SNE plot Scater: PCA plot Scater: plot expression frequency Scater: plot library QC Scater: normalize SCE Scater: filter SCE Scater: calculate QC metrics Cluster Inspection using RaceID Initial processing using RaceID Clustering using RaceID Lineage computation using StemID Lineage Branch Analysis using StemID
MarkDuplicatesWithMateCigar ReorderSam MarkDuplicates SortSam AddOrReplaceReadGroups QualityScoreDistribution CleanSam MeanQualityByCycle CollectBaseDistributionByCycle NormalizeFasta EstimateLibraryComplexity Collect Alignment Summary Metrics CollectWgsMetrics FastqToSam MergeBamAlignment FilterSamReads CollectRnaSeqMetrics RevertOriginalBaseQualitiesAndAddMateCigar ValidateSamFile CollectGcBiasMetrics Downsample SAM/BAM SamToFastq RevertSam BedToIntervalList MergeSamFiles FixMateInformation AddCommentsToBam CollectInsertSizeMetrics ReplaceSamHeader SAM/BAM Alignment Summary Metrics BAM Index Statistics Add or Replace Groups Estimate Library Complexity Insertion size metrics Paired Read Mate Fixer CollectHsMetrics Picard Collect Sequencing Artifact Metrics bamCompare bamCoverage bamPEFragmentSize bigwigCompare plotHeatmap correctGCBias multiBamSummary plotPCA computeMatrix computeGCBias multiBigwigSummary plotProfile plotCorrelation plotCoverage plotFingerprint computeMatrixOperations alignmentsieve plotEnrichment estimateReadFiltering 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 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 Diamond Diamond makedb Diamond view Magic-BLAST: map large RNA or DNA sequences Krona pie chart BLAST XML to tabular NCBI BLAST+ database info NCBI BLAST+ blastdbcmd entry(s) NCBI BLAST+ blastn NCBI BLAST+ blastp NCBI BLAST+ blastx NCBI BLAST+ convert2blastmask NCBI BLAST+ dustmasker NCBI BLAST+ makeblastdb NCBI BLAST+ makeprofiledb NCBI BLAST+ rpsblast NCBI BLAST+ rpstblastn NCBI BLAST+ segmasker NCBI BLAST+ tblastn NCBI BLAST+ tblastx Kraken-translate Kraken-filter BLAST Reciprocal Best Hits (RBH) Sub-sample sequences files BLAST top hit descriptions BBTools: BBMap BBTools: call variants BBTools: BBduk Kraken taxonomic report NCBI get species taxids 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 hicHyperoptDetectLoops hicDifferentialTAD hicMergeDomains Stacks2: process shortreads Stacks2: reference map Stacks2: de novo map Stacks2: cstacks Stacks2: kmer filter Stacks2: tsv2bam Stacks2: process radtags Stacks2: gstacks Stacks2: ustacks BayeScan Stacks: assemble read pairs by locus Stacks: cstacks Stacks2: clone filter Stacks2: populations Stacks2: sstacks 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
MALT analyzer ITSx CoverM-CONTIG CoverM-GENOME MEGAN: Extract reads MEGAN: Generate a MEGAN rma6 file MEGAN: Get information CONCOCT: extract a fasta file CONCOCT coverage table CONCOCT Phyloseq: plot ordination Create phyloseq object Kraken2 dada2: makeSequenceTable dada2: plotQualityProfile dada2: mergePairs dada2: assignTaxonomy and addSpecies dada2: sequence counts dada2: plotComplexity dada2: learnErrors dada2: dada dada2: removeBimeraDenovo dada2: filterAndTrim MetaEuk Easy Predict staramr LAST-train MT2MQ Join VSearch search HUMAnN2 Associate Binning refiner Phyloseq: plot alpha diverstiy measure CONCOCT: cut fasta contigs Barplot MEGAN: meganize a DIAMOND file CONCOCT: merge cut clusters Create a genus level gene families file Reduce Regroup Rename Renormalize Normalize Split stratified table Split Make strain profiles Unpack pathway abundances to show genes included LASTal dRep dereplicate dRep compare LASTdb LAST-split MAF-convert mash screen MetaGeneAnnotator mash sketch sixgill merge sixgill filter sixgill build sixgill makefasta CAT contigs CAT bins khmer: Filter reads khmer: Filter reads khmer: Extract partitions khmer: Abundance Distribution khmer: Count Median khmer: Sequence partition all-in-one khmer: Normalize By Median khmer: Abundance Distribution (all-in-one) Kraken Kraken-report Krona pie chart Kraken-filter Kraken-translate CAT add_names CAT summarise CAT prepare MaxBin2 Group abundances PlasFlow Kraken-mpa-report Vegan Diversity Vegan Fisher Alpha Vegan Rarefaction VSearch sorting VSearch chimera detection VSearch clustering VSearch masking VSearch alignment VSearch dereplication VSearch shuffling Compare outputs of HUMAnN2 for several samples Combine MetaPhlAn2 and HUMAnN2 outputs Format MetaPhlAn2 VALET GDCWebApp Salmonella Subtyping Nonpareil MetaPhlAn2 Format MetaPhlAn2 Merge Generate heatmap metagenomeSeq Normalization Kraken taxonomic report 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 Extract the marker sequences and metadata Customize the marker sequences and metadata LotuS2 InStrain Profile InStrain Compare Estimate Abundance at Taxonomic Level MaAsLin 2 MEGAN: Generate a MEGAN rma6 file MEGAN: Generate RMA files MEGAN Blast2LCA: apply LCA alignment Calculate contig depths MetaBAT2 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 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 obitab obistat obisort obiconvert obiclean obiuniq obigrep obiannotate NGSfilter Illuminapairedend ivar consensus ivar removereads ivar trim ivar getmasked ivar variants ivar filtervariants Read It and Keep
MaxQuant MSstatsTMT MSstats ConsensusID metaQuantome: visualize metaQuantome: stat metaQuantome: filter metaQuantome: expand metaQuantome: database eggNOG Mapper MSI combine PSMFeatureExtractor MetaProteomeAnalyzer metaQuantome: create samples file pyteomics DIAlignR FASTG2Protlib-Peptides FASTG2Protlib-Validate NovorAdapter LuciphorAdapter AssayGeneratorMetabo SiriusAdapter MSFraggerAdapter MSGFPlusAdapter MSI plot spectra MSI mz images MSI preprocessing PeakPickerHiRes RNAMassCalculator QualityControl RNPxlXICFilter OpenSwathConfidenceScoring MultiplexResolver PSM-Fragment Validator Remove protonation state idpQuery OpenSwathFeatureXMLToTSV OpenSwathDIAPreScoring MapStatistics DigestorMotif FeatureLinkerLabeled XTandemAdapter SpectraFilterWindowMower OpenSwathWorkflow QCMerger IDMapper IDMassAccuracy IDRTCalibration IDSplitter MRMTransitionGroupPicker MapAlignerIdentification IsobaricAnalyzer ERPairFinder ClusterMassTraces ClusterMassTracesByPrecursor CometAdapter CompNovo CompNovoCID IDMerger MetaboliteSpectralMatcher MetaNovo ProteomIQon MzMLToMzLite Proteomiqon PSMBasedQuantification RTEvaluation QCExporter SpectraFilterNormalizer InternalCalibration MassTraceExtractor Digestor PepNovoAdapter PeptideIndexer MapRTTransformer DTAExtractor OpenSwathAssayGenerator MetaProSIP SequenceCoverageCalculator ProteinQuantifier IDConflictResolver PeakPickerWavelet FuzzyDiff PeakPickerIterative Decharger MzMLSplitter FileConverter SpectraFilterNLargest MassCalculator SpectraFilterThresholdMower MapAlignerPoseClustering QCEmbedder Epifany SpectraMerger PTModel OpenSwathDecoyGenerator ProteinInference TargetedFileConverter TextExporter TOFCalibration TransformationEvaluation IDRipper XMLValidator SvmTheoreticalSpectrumGeneratorTrainer MascotAdapterOnline SpectraSTSearchAdapter SpectraFilterSqrtMower SpectraFilterMarkerMower SemanticValidator SpecLibSearcher LabeledEval MapAlignerSpectrum SpecLibCreator MaRaClusterAdapter SimpleSearchEngine PrecursorIonSelector SeedListGenerator RTModel FeatureFinderCentroided RNPxlSearch SpectraFilterParentPeakMower TICCalculator IDFilter NucleicAcidSearchEngine MRMMapper OMSSAAdapter EICExtractor MyriMatchAdapter SpectraFilterBernNorm MSSimulator BaselineFilter RNADigestor CVInspector MSI Qualitycontrol DecoyDatabase ExternalCalibration FalseDiscoveryRate FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMRM FeatureFinderMultiplex FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FFEval FidoAdapter FileFilter FileInfo FileMerger GNPSExport AccurateMassSearch DatabaseFilter DeMeanderize FeatureFinderSuperHirn MSI classification OpenSwathMzMLFileCacher OpenSwathRewriteToFeatureXML IDPosteriorErrorProbability IDFileConverter MSI data exporter MSI segmentation MSI filtering IDScoreSwitcher OpenPepXL XFDR MapAlignerTreeGuided PercolatorAdapter MapNormalizer MascotAdapter MetaboliteAdductDecharger MRMPairFinder MSstatsConverter MzTabExporter NoiseFilterGaussian EncyclopeDIA NoiseFilterSGolay ConvertFastaToPrositCSV EncyclopeDIA Quantify OpenPepXLLF Walnut ConvertPrositCSVToLibrary OpenSwathChromatogramExtractor OpenSwathAnalyzer SearchToLib OpenSwathFileSplitter ConvertLibraryToBlib OpenSwathRTNormalizer PhosphoScoring HighResPrecursorMassCorrector PrecursorMassCorrector QCCalculator CruxAdapter ConsensusMapNormalizer QCShrinker QCImporter SpectraFilterScaler IDExtractor QCExtractor ProteinResolver LowMemPeakPickerHiRes LowMemPeakPickerHiResRandomAccess MT2MQ PepQuery MyriMatch idpEmbedder idpQonvert idpAssemble PyProphet export moFF Unipept MALDIquant peak detection PyProphet score Kronik Hardklor diapysef library generation PyProphet merge PyProphet peptide PyProphet protein PyProphet subsample Proteinortho summary Proteinortho grab proteins Proteinortho FlashLFQ QuantWiz-IQ Peptide Genomic Coordinate Pathway Matcher MaxQuant (using mqpar.xml) 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 TopPerc Protease prediction Create Decoy Database (reverse) Morpheus FastaCLI Identification Parameters Diffacto ProteomIQon PeptideDB ProteomIQon PeptideSpectrumMatching ProteomIQon PSMStatistics ProteomIQon ProteinInference MaxQuant (using mqpar.xml) Validate FASTA Database Proteomiqon JoinQuantPepIonsWithProteins Proteomiqon LabeledProteinQuantification Proteomiqon LabelFreeProteinQuantification TRIC X!Tandem MSMS Search OrthoFinder MSI single ion segmentation MSI colocalization X!Tandem MSMS Search 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 xcms refineChromPeaks (refine) Isoplot: Generate plots from isocor output Modify/convert GROMACS trajectories 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 GROMACS simulation GROMACS energy minimization GROMACS initial setup Substructure Search Hierarchical clustering Extract clusters of MD trajectories Extract RMSD distance matrix data Add hydrogen atoms Remove counterions and fragments ChEMBL structure pipeline dcTMD friction correction Remove protonation state Ramachandran Analysis End-to-End Analysis Cosine Content Hydrogen Bond Analysis Ramachandran Plots Distance Analysis Dihedral Analysis OpenPepXL Change title RDF Analysis Spectrophores search Angle Analysis APoc smina Prepare receptor Enumerate changes Extract values from an SD-file fpocket Calculate molecular descriptors PubChem Download PubChem Assay Downloader VINA Docking Prepare ligand Calculate the box parameters using RDKit Remove duplicated molecules Filter Compound conversion Visualisation Compute physico-chemical properties Compound search Remove small molecules Prepare ligands for docking Descriptors Drug-likeness Score docked poses using SuCOS Cluster ligands using SuCOS Max SuCOS score Determine distance to defined points Create Frankenstein ligand rDock cavity definition rDock docking rDock docking rxDock cavity definition rxDock docking SDF sort and filter Calculate plane of best fit for molecules Reaction SMARTS filter Generate conformers Constrained conformer generation Butina Cluster Matrix Open 3D Align Standardize SD-files Butina Cluster Pick Reaction maker Screen XCos 'FeatureStein' fragment overlay scoring Merge GROMACS topologies OpenDUck chunk Run OpenDUck XChem TransFS pose scoring Molecule to fingerprint NxN clustering Taylor-Butina clustering SDF to Fingerprint MDTraj file converter fastpca RDConf: Low-energy ligand conformer search Trajectory select and merge Alchemical Analysis 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 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
Create a model to recommend tools MINE Draw ROC plot Perform LDA Generate A Matrix Count GFF Features Correlation Perform Best-subsets Regression Principal Component Analysis Kernel Principal Component Analysis Kernel Canonical Correlation Analysis Canonical Correlation Analysis T Test for Two Samples Sparse Matrix Functions Wavelet variance GraphEmbed Landmark Registration Plot actual vs predicted curves and residual plots Plot confusion matrix, precision, recall and ROC and AUC curves Rolling window Nearest Neighbors Classification Support vector machines (SVMs) Anova Multivariate Univariate IWTomics Plot with Threshold IWTomics Test IWTomics Load Sequence composition Biosigner Transformation Heatmap RGCCA Statistical hypothesis testing Summary Statistics Count Principal component analysis LightGBM Numeric Clustering Stacking Ensembles Deep learning training and evaluation Machine Learning Visualization Extension Support vector machines (SVMs) Train, Test and Evaluation Model Prediction Generate Estimator attributes Hyperparameter Search Pipeline Builder Evaluate pairwise distances Nearest Neighbors Classification Ensemble methods Feature Selection Preprocess Calculate metrics Calculate metrics Discriminant Analysis Generalized linear models Model Validation Evaluate a Fitted Model Fit a Pipeline, Ensemble Split Dataset Build Deep learning Batch Training Models Create deep learning model Create a deep learning model architecture Sparse Matrix Functions Create a model to recommend tools To categorical Pathview Build custom track Scatterplot Histogram GMAJ Plotting tool BAM Coverage Plotter JBrowse - Data Directory to Standalone JBrowse pyGenomeTracks Circos: Interval to Tiles Circos: Resample 1/2D data Circos: Link Density Track Circos: bigWig to Scatter Circos: Interval to Circos Text Labels Circos: Alignments to links Circos: Table viewer Circos GC Skew Circos: Stack bigWigs as Histogram Circos: Bundle Links Heatmap w ggplot Violin plot w ggplot2 Scatterplot with ggplot2 Histogram with ggplot2 Plot confusion matrix, precision, recall and ROC and AUC curves Newick Display Bandage Info Bandage Image UpSet diagram Pairwise intersection Krona pie chart Export to GraPhlAn Venn Diagram Volcano Plot heatmap2 Plot actual vs predicted curves and residual plots Parallel Coordinates Plot PCA plot w ggplot2 Fasta nucleotide color plot GraPhlAn Generation, personalization and annotation of tree rtsne Visualize with Krona Fasta nucleotide color plot MUMmer dotplot Karyotype Plotting tool Paired-end histogram Pretext Snapshot Bar chart Boxplot LAJ VCF to MAF Custom Track
TN93 Cluster TN93 Filter Mutate Codons IQ-TREE codeML Structure Join neighbors TN93 Merge matching reads aaChanges phyloP FIMO MEME Sequence Logo MEME psp-gen DREME MEME-ChIP Personal Cancer Genome Reporter 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 Discriminant Analysis Convert Transform Nearest Neighbors Classification Numeric Clustering Support vector machines (SVMs) Sparse Matrix Functions Preprocess Evaluate pairwise distances Generate Ensemble methods Calculate metrics Protease prediction bwtool-lift Calculate protein properties Base Count Codon count GenBank and EBML Extract sequences from GenBank GFF converter Sequence converter Translate nucleotides RNALfoldz HE/ MALDI Image Registration NetCDF xarray Metadata Info NetCDF xarray Selection OGR Informations OGR2ogr GDAL Warp GDAL Translate GDAL Merge GDAL Informations GDAL Build VRT GDAL addo NetCDF xarray operations NetCDF xarray map plotting NetCDF xarray Coordinate Info 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 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 CTSM/FATES-EMERALD climate stripes map plot Copernicus Essential Climate Variables zonal statistics shift longitudes Copernicus Climate Data Store CESM Copernicus Atmosphere Data Store EODIE CDO Operations CDO get info 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 Association of points CellProfiler Starting Modules ColorToGray Tile TrackObjects OverlayOutlines ConvertObjectsToImage DisplayDataOnImage EnhanceOrSuppressFeatures ExportToSpreadsheet GrayToColor IdentifyPrimaryObjects MaskImage MeasureGranularity MeasureImageAreaOccupied MeasureImageIntensity MeasureImageQuality MeasureObjectIntensity MeasureObjectSizeShape MeasureTexture RelateObjects SaveImages Spot Detection ImageMath Landmark Registration Image Registration Projective Transformation SpyBOAT Convert binary image to EDM Skeletonize Find edges Add shadow effect Enhance contrast Find maxima Watershed segmentation Apply raw transformation Operate on pixels Apply elastic transformation IDR/OMERO Download 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 Curve Fitting Overlay Images 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 Interactive Jupyter Notebook GPU enabled Interactive Jupyter Notebook for Machine Learning Interactive Climate Notebook Interactive Pangeo Notebook RStudio PyIron Interactive Jupyter Notebook HiGlass OpenRefine Ubuntu XFCE Desktop Panoply AskOmics Interactive CellXgene Environment bam.iobio visualisation VCF (iobio) Visualisation Neo4j (Graph Database) Phinch Visualisation Paraview Wilson Wallace geoexplorer radiant EtherCalc VRM Editor SimText iSEE metashark 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 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 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 Spatial coordinates anonymization Local Contributions to Beta Diversity (LCBD) Homoscedasticity and normality Variables exploration Presence-absence and abundance Statistics on presence-absence tracy Basecall tracy Align tracy Decompose tracy Assemble Gene length and GC content 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