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Faster Download and Extract Reads in FASTQ NCBI Accession Download UniProt Unipept IEDB Download and Extract Reads in BAM Protein Database Downloader NCBI Datasets Genomes Download and Generate Pileup Format Get species occurrences data 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 EGA Download Client 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 Export datasets Export datasets ENA Upload tool cURL Collapse Collection Split file Split file 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 Calculate numeric parameter value Compose text parameter value Parse parameter value
Table Compute diff Histogram Compute Concatenate datasets Replace column Add line to file Text reformatting Add input name as column Merge Columns Switch axis coordinates Replace Sort a row Column Regex Find And Replace Regex Find And Replace Join two files PRINSEQ 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 Cluster Rebase GFF3 features Remove columns Sort Column Order Unique Select first Multi-Join Select last Advanced Cut Create text file 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
twoBitToFa CrossMap BAM Stitch Gene blocks ab1 to FASTQ converter mz to sqlite Convert Convert BAM samtools BAM to CRAM gffread CrossMap region idpQuery Thermo Tabular-to-FASTA bax2bam CrossMap BED CrossMap GFF CrossMap VCF CrossMap Wig Compress file(s) FASTA-to-Tabular Tabular to FASTQ GFA to FASTA msconvert Extract MAF blocks bed to protein map Convert gffCompare annotated GTF to BED Map peptides to a bed file Resize coordinate window msms_extractor Image Montage Image Converter Create InterMine Interchange idconvert msconvert Subset Peak List idconvert Convert GTF to BED12 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 Cutadapt fastp Clip UMI-tools whitelist UMI-tools group Fasta Statistics UMI-tools deduplicate UMI-tools count Trim Galore! UMI-tools extract RNA-seq Rcorrector FASTQE FastQC faSplit Trimmomatic Select high quality segments filtlong 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 Filter sequences by length FASTA-to-Tabular Tabular to FASTQ Tabular-to-FASTA Remove sequencing artifacts Exonerate Sickle seqtk_sample 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 Draw nucleotides distribution chart Barcode Splitter Get crosslinked nucleotides Trim putative adapter sequence Create binary barcodes Extract barcodes Extract alignment ends Merge PCR duplicates Remove spurious Remove 3'-end nts Je-Clip Je-Demultiplex Je-MarkDuplicates Je-Demultiplex-Illu FASTA Merge Files and Filter Unique Sequences Thread nucleotides onto a protein alignment (back-translation) Filter sequences by mapping lighter fastq-join Split Fasta Split Fasta Convert Compute quality statistics Draw quality score boxplot MultiQC FASTQ info QualiMap Counts QC Samtools coverage Convert, Merge, Randomize Filter Split BAM by Paired/Single End Split BAM by Reference Split BAM by Mapped Split BAM by Tag Samtools phase Samtools fastx Samtools view Samtools stats Samtools split Samtools flagstat Samtools markdup Slice Samtools idxstats Samtools sort Samtools bedcov BamUtil diff Pileup-to-Interval Samtools reheader QualiMap BamQC Convert SAM Generate pileup QualiMap Multi-Sample BamQC Split Tag pileup frequency Samtools mpileup Samtools calmd Samtools merge Samtools depth Samtools fixmate Filter SAM or BAM, output SAM or BAM BAM filter RmDup Merge BAM Files BamHash bedtools AnnotateBed bedtools BAM to BED bedtools BED12 to BED6 bedtools BED to BAM bedtools BED to IGV bedtools BEDPE to BAM bedtools ClosestBed bedtools ClusterBed bedtools ComplementBed bedtools Compute both the depth and breadth of coverage bedtools ExpandBed bedtools FisherBed bedtools FlankBed bedtools Genome Coverage bedtools GetFastaBed bedtools GroupByBed bedtools Intersect intervals bedtools JaccardBed bedtools LinksBed bedtools MakeWindowsBed bedtools MapBed bedtools MaskFastaBed bedtools MergeBED bedtools MultiCovBed bedtools Multiple Intersect bedtools NucBed bedtools OverlapBed bedtools RandomBed bedtools ReldistBed bedtools ShuffleBed bedtools SlopBed bedtools SortBED bedtools SpacingBed bedtools SubtractBed bedtools TagBed bedtools Merge BedGraph files bedtools WindowBed GffCompare bedtools Convert from BAM to FastQ Create a BedGraph of genome coverage Merge BedGraph files Create a histogram of genome coverage vcfanno VarScan somatic VarScan copynumber bcftools csq bcftools cnv bcftools consensus bcftools norm bcftools call VCFcheck: VCFfilter: 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: VarScan VarScan mpileup bcftoolsView FreeBayes VCFdistance: Naive Variant Caller (NVC) snippy snippy-core ococo BamLeftAlign VCFdistance: Variant Annotator Merge Intersect VT normalize bcftools view Compare Annotate Slice VCF Subset medaka variant pipeline ont_fast5_api: Multi to single ont_fast5_api: Compress medaka variant tool medaka consensus tool FLAIR correct Porechop Pycoqc FLAIR collapse CoNvex medaka consensus pipeline NanoComporeDB ont_fast5_api: Subset ont_fast5_api: Single to multi NanoPlot Nanopolish polyA Nanopolish eventalign Nanopolish methylation Nanopolish variants SampComp NanopolishComp: FreqMethCalculate NanopolishComp: EventalignCollapse Extract time Show nucleotide Show quality Extract reads Extract FASTQ Read length statistics Plot signals Plot performance Generate histogram Collector’s curve Generate box-whisker Get longest read Extract nanopore events
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
KofamScan Maker InterProScan Roary progressiveMauve TRANSIT HMM Convert GFF3 GECCO OrthoFinder List spaln parameter tables Spaln: align cDNA or Protein to genome Prokka Busco summarize hamronize RepeatMasker findMotifsGenome annotatePeaks Funannotate functional Funannotate predict annotation TB Variant Filter Train Augustus Augustus ChIPseeker SpoTyping lorikeet spoligotyping TB-Profiler Profile hmmbuild hmmscan annotateMyIDs TB Variant Report goseq Map annotation ids Glimmer3 Glimmer3 Glimmer ICM builder MITOS2 sistr_cmd HHsearch ABRicate Summary OptiType nhmmer phmmer jackhmmer nhmmscan RepeatModeler hmmsearch Table to GFF3 scanMotifGenomeWide hmmemit hmmalign Converts GTF to Annotations file for Homer Funannotate assembly clean Sort assembly Funannotate compare hmmfetch alimask hmmconvert MOB-Recon MOB-Typer seq2HLA TRANSIT Gumbel TRANSIT Resampling TRANSIT Tn5Gaps MITOS ectyper Antismash Convert XMFA to gapped GFF3 MLST List MLST Genbank to GFF3 ABRicate List ABRicate Exonerate FastANI TETyper fargene KOBAS Annotate KOBAS Identify gProfiler SNPense gProfiler Random gProfiler GOSt gProfiler Orth gProfiler Convert BlastXML to gapped GFF3 Compute socru Train SNAP fgsea Filter with SortMeRNA 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 CryptoGenotyper Interproscan functional predictions of ORFs Annotate with DGI Annotate with DGI SnpSift GeneSets DNAdiff Nucmer Delta-Filter Mummerplot Mummer cd-hit MAFFT add MAFFT Show-Coords Chromeister ClustalW SINA Gecko MAF Coverage Stats Kc-Align Automated multiple sequence Select Sequences MSABOOT Hammock - cluster peptides Format cd-hit outputs MUSCLE Compalignp biosyntheticSPAdes coronaSPAdes metaplasmidSPAdes metaviralSPAdes plasmidSPAdes rnaviralSPAdes SPAdes metaSPAdes Quast MEGAHIT Bionano Hybrid Scaffold ABySS rnaSPAdes Trycycler cluster Trycycler consensus Trycycler partition Trycycler reconcile/msa Trycycler subsample NOVOplasty Minia Flye HyPo TGS-GapCloser SALSA PretextMap RagTag Purge overlaps Raven Hifiasm Meryl GenomeScope MitoHiFi Filter and merge DISCO Merqury miniasm Canu assembler Racon Shovill Lordec MITObim TrimN AEGeAn ParsEval AEGeAn LocusPocus AEGeAn GAEVAL AEGeAn CanonGFF3 Shasta IDBA-TRAN Create assemblies with Unicycler IDBA-UD IDBA-HYBRID VelvetOptimiser pilon WTDBG Assemble with MIRA v3.4 Edena (assembling) Edena (overlapping) SOPRA with prebuilt contigs SSAKE CRISPR Recognition Tool detect CRISPR sequences velvetg velveth Bowtie2 BBTools: BBMap Map with KMA Map with minimap2 Align sequences HISAT2 Winnowmap RNA STAR Map with BWA-MEM LASTZ RNA STARSolo Parse blast XML output Megablast Lastz paired reads Map with Bowtie for Illumina BWA-MEM2 LASTZ_D Bismark Mapper STAR-Fusion Bismark Deduplicate Bismark Pretty Report Bismark Meth. Extractor segemehl Owler Mapper Bismark Map with BWA TopHat Map with Bowtie for SOLiD Map with BFAST Map with PerM Re-align with SRMA Map with Mosaik BBTools: call variants pharmCAT plink seqwish bcftools annotate FreeBayes BamLeftAlign bcftools convert from vcf bcftools filter bcftools gtcheck bcftools isec bcftools reheader bcftools view bcftools mpileup VCFcheck: VarScan somatic VarScan copynumber VarScan mpileup Delly filter Delly merge Delly long-read (lr) Delly classify Delly cnv Control-FREEC bcftools stats GATK4 Mutect2 DeepVariant snippy-core snippy snippy-clean_full_aln LUMPY Beagle bcftools roh Iris JasmineSV sansa annotate Strelka Germline Get homopolymer run length Strelka Somatic bcftools query LUMPY preprocessing bcftools convert to vcf bcftools cnv KING VarDict Delly call bcftools concat ARTIC guppyplex bcftools merge ARTIC minion bcftools consensus vcfanno Variant Frequency Plot DCS mutations to tags/reads: SnpSift Filter DCS mutations to SSCS stats: Call specific mutations in reads: Lofreq filter Call variants cuteSV sniffles SnpEff eff: Realign reads Add LoFreq alignment quality scores Insert indel qualities odgi viz odgi build vg view vg deconstruct vg convert VCFselectsamples: VCFannotateGenotypes: VCFdistance: VCFflatten: VCFcommonSamples: VCFannotate: VCF-VCFintersect: VCFbreakCreateMulti: VcfAllelicPrimitives: VCFgenotype-to-haplotype: VCFfilter: VCFfixup: VCFgenotypes: VCF-BEDintersect: VCFrandomSample: VCFhetHomAlleles: VCFsort: VCFprimers: VCFcombine: VCFleftAlign: VCFtoTab-delimited: VCFaddinfo: bcftools call SnpEff chromosome-info: bcftools norm bcftools csq bcftools frameshifts bcftools color-chrs SNP distance matrix Tag pileup frequency Finds SNP sites ExomeDepth 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 SnpEff Ensembl CDS SnpEff to Peptide fasta Naive Variant Caller Variant Annotator SnpSift Intervals SnpSift Annotate SnpSift Filter SnpSift CaseControl CRISPR Studio parse mykrobe predict AmpliCan MAGeCKs test MAGeCK mle MAGeCK GSEA MAGeCK count MAGeCK pathway blockbuster Generate gene to transcript map Trinotate edgeR limma ChiRA qauntify ChiRA merge ChiRA map ChiRA collapse Filter low expression transcripts Compute contig Ex90N50 statistic and Ex90 transcript count Generate SuperTranscripts DEXSeq Align reads and estimate abundance DEXSeq-Count plotDEXSeq StringTie StringTie merge tximport Trinity Seurat TransDecoder cmalign cmbuild cmpress cmscan DESeq2 cmsearch cmstat Alleyoop Slamdunk Cuffmerge Salmon quantmerge featureCounts EGSEA TargetFinder MiGMAP Kallisto pseudo Kallisto quant Remove Unwanted Variation Salmon quant rnaQUAST GenomicSuperSignature Filter Combined Transcripts eXpress ChiRA extract maSigPro Cufflinks Cuffdiff Cuffcompare FEELnc scPipe TEtranscripts footprint Cuffnorm cummeRbund htseq-count Differential expression analysis Build expression matrix sRNAPipe GraphProt Visualize QualiMap Counts QC QualiMap RNA-Seq QC Filter with SortMeRNA GLASSgo IntaRNA Cross-contamination Barcode Filter Extract and cluster differentially expressed transcripts 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 Get motifs from AREsite2 FuMa RNAlien BlockClust 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 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 CCAT MACS SICER 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 bwameth MethylDackel 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 Pangolin NextAlign Nextclade HyPhy-BUSTED HyPhy-aBSREL SNP distance matrix HyPhy-Summary HyPhy-RELAX Replace ambiguous codons HyPhy-FUBAR HyPhy-GARD HyPhy-FEL HyPhy-SLAC HyPhy-MEME HyPhy-PRIME HyPhy-BGM HyPhy-CFEL HyPhy-FADE HyPhy-SM2019 HyPhy-Conv Annotate UShER matUtils UShER sarscov2formatter T-Coffee 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 VCF to pgSnp snpFreq FunDO HVIS Separate pgSnp alleles CTD aaChanges phyloP SIFT g:Profiler DAVID LD PASS GPASS BEAM LPS MasterVar to pgSnp Construct Expression Set Object MuSiC Deconvolution MuSiC Compare Cluster Inspection using RaceID Initial processing using RaceID Clustering using RaceID Lineage computation using StemID Lineage Branch Analysis using StemID Scater: PCA plot Scater: filter SCE Scater: t-SNE plot Scater: calculate QC metrics Scater: plot library QC Alevin DropletUtils Plot Inspect and manipulate Cluster, infer trajectories and embed Import Anndata and loom Export AnnData and loom files Manipulate AnnData Inspect Expression Set Object Filter Normalize Inspect AnnData Remove confounders Manipulate loom object DropletUtils Read10x DropletUtils emptyDrops Slice Image Scanpy ParameterIterator Scater: plot expression frequency Scater: normalize SCE
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 bamCompare bamPEFragmentSize multiBamSummary computeMatrix plotEnrichment bamCoverage bigwigCompare plotHeatmap correctGCBias alignmentsieve computeMatrixOperations plotFingerprint plotCoverage plotCorrelation plotProfile multiBigwigSummary computeGCBias plotPCA 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 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 fuzznuc 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 cpgplot notseq seqret plotorf cai btwisted newseq chaos pepnet textsearch chips garnier cusp descseq cirdna tmap sirna coderet biosed BBTools: BBduk Diamond Diamond makedb Diamond view Krona pie chart BBTools: BBMap BBTools: call variants 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 hicPlotViewpoint hicPlotMatrix hicFindTADs hicCompareMatrices hicAggregateContacts hicNormalize hicSumMatrices hicConvertFormat hicAdjustMatrix hicInfo hicHyperoptDetectLoops scHicQualityControl chicPlotViewpoint chicDifferentialTest chicAggregateStatistic chicSignificantInteractions chicViewpoint hicDifferentialTAD hicMergeDomains chicQualityControl hicFindRestSite chicViewpointBackgroundModel hicQuickQC hicBuildMatrix hicMergeMatrixBins hicTransform hicCompartmentalization hicCorrelate hicDetectLoops hicMergeLoops hicValidateLocations hicCorrectMatrix hicPCA hicPlotAverageRegions hicPlotDistVsCounts hicAverageRegions hicPlotSVL scHicCorrectMatrices scHicPlotConsensusMatrices scHicPlotClusterProfiles scHicNormalize scHicCreateBulkMatrix scHicMergeToSCool scHicMergeMatrixBins scHicInfo scHicDemultiplex scHicConsensusMatrices scHicClusterSVL scHicClusterMinHash scHicClusterCompartments scHicCluster scHicAdjustMatrix hicPlotTADs Stacks2: process shortreads Stacks2: reference map Stacks2: de novo map Stacks2: process radtags Stacks2: populations Stacks2: gstacks Stacks2: ustacks Stacks2: kmer filter Stacks2: clone filter Stacks2: tsv2bam Stacks2: sstacks BayeScan Stacks: assemble read pairs by locus Stacks: cstacks Stacks2: cstacks 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
dRep compare LotuS2 Customize the marker sequences and metadata Merge Calculate contig depths LASTal MALT analyzer MaAsLin 2 Estimate Abundance at Taxonomic Level MetaEuk Easy Predict Kraken2 Kraken Kraken-report Kraken-mpa-report MEGAN: Generate a MEGAN rma6 file MEGAN: Generate RMA files MEGAN Blast2LCA: apply LCA alignment MetaPhlAn Extract the marker sequences and metadata dRep dereplicate MetaBAT2 Convert Kraken Kraken-translate Kraken-filter Krona pie chart Kraken taxonomic report InStrain Profile dada2: plotQualityProfile dada2: mergePairs dada2: assignTaxonomy and addSpecies dada2: makeSequenceTable dada2: learnErrors dada2: removeBimeraDenovo dada2: dada dada2: filterAndTrim Make strain profiles Split a HUMAnN table Rename features Join (merge) Perform metadata association Regroup HUMAnN Split Renormalize Barplot Salmonella Subtyping jellyfish HUMAnN2 LASTdb LAST-split LAST-train MAF-convert khmer: Abundance Distribution (all-in-one) khmer: Sequence partition all-in-one khmer: Count Median khmer: Abundance Distribution khmer: Filter reads khmer: Filter reads staramr Scoary khmer: Extract partitions khmer: Normalize By Median Reduce Normalize Unpack pathway abundances mash screen dada2: sequence counts dada2: plotComplexity InStrain Compare MT2MQ Join VSearch search Associate Barplot 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 MetaGeneAnnotator mash sketch sixgill merge sixgill filter sixgill build sixgill makefasta CAT contigs CAT bins CAT add_names CAT summarise CAT prepare MaxBin2 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 Nonpareil MetaPhlAn2 Format MetaPhlAn2 Generate heatmap metagenomeSeq Normalization 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 obistat obisort obiconvert obiclean obiuniq obigrep obiannotate Illuminapairedend NGSfilter obitab Read It and Keep ivar removereads ivar trim ivar variants ivar filtervariants ivar consensus ivar getmasked
eggNOG Mapper Proteinortho summary OpenPepXL XFDR PercolatorAdapter metaQuantome: create samples file FastaCLI Identification Parameters MaxQuant (using mqpar.xml) Search GUI Proteinortho Proteomiqon LabeledProteinQuantification Proteomiqon JoinQuantPepIonsWithProteins Proteomiqon PSMBasedQuantification MSI combine MSI plot spectra MSI preprocessing MSI Qualitycontrol MSI mz images MSI data exporter MSI segmentation MSI filtering ProteomIQon PSMStatistics MSstats ProteomIQon ProteinInference MSstatsTMT Peptide Shaker ProteomIQon PeptideDB MaxQuant ProteomIQon MzMLToMzLite Diffacto MSI classification metaQuantome: visualize metaQuantome: stat metaQuantome: expand idpAssemble idpEmbedder idpQonvert ConvertFastaToPrositCSV EncyclopeDIA Quantify Walnut SearchToLib ConvertLibraryToBlib PepQuery Peptide Genomic Coordinate ConsensusID ConvertPrositCSVToLibrary MyriMatch EncyclopeDIA metaQuantome: database MaxQuant (using mqpar.xml) metaQuantome: filter ProteomIQon PeptideSpectrumMatching Proteinortho grab proteins OrthoFinder Validate FASTA Database Proteomiqon LabelFreeProteinQuantification TRIC PSMFeatureExtractor MetaProteomeAnalyzer pyteomics DIAlignR FASTG2Protlib-Peptides FASTG2Protlib-Validate NovorAdapter LuciphorAdapter AssayGeneratorMetabo SiriusAdapter MSFraggerAdapter MSGFPlusAdapter 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 RTEvaluation QCExporter SpectraFilterNormalizer InternalCalibration MassTraceExtractor PepNovoAdapter Digestor PeptideIndexer MapRTTransformer OpenSwathAssayGenerator DTAExtractor SequenceCoverageCalculator MetaProSIP IDConflictResolver PeakPickerWavelet ProteinQuantifier PeakPickerIterative Decharger FuzzyDiff MzMLSplitter FileConverter MassCalculator SpectraFilterNLargest MapAlignerPoseClustering QCEmbedder Epifany SpectraFilterThresholdMower SpectraMerger OpenSwathDecoyGenerator PTModel TargetedFileConverter TextExporter TOFCalibration TransformationEvaluation XMLValidator ProteinInference SvmTheoreticalSpectrumGeneratorTrainer IDRipper SpectraSTSearchAdapter SpectraFilterSqrtMower SpectraFilterMarkerMower SpecLibSearcher MascotAdapterOnline MapAlignerSpectrum SpecLibCreator SemanticValidator SimpleSearchEngine LabeledEval SeedListGenerator RTModel MaRaClusterAdapter RNPxlSearch PrecursorIonSelector FeatureFinderCentroided SpectraFilterParentPeakMower TICCalculator MRMMapper OMSSAAdapter EICExtractor MyriMatchAdapter IDFilter MSSimulator BaselineFilter NucleicAcidSearchEngine SpectraFilterBernNorm CVInspector RNADigestor DecoyDatabase ExternalCalibration FalseDiscoveryRate FeatureFinderIdentification FeatureFinderIsotopeWavelet FeatureFinderMetabo FeatureFinderMetaboIdent FeatureFinderMRM FeatureFinderMultiplex FeatureLinkerUnlabeled FeatureLinkerUnlabeledKD FeatureLinkerUnlabeledQT FFEval FidoAdapter FileFilter FileInfo FileMerger GNPSExport AccurateMassSearch DatabaseFilter DeMeanderize FeatureFinderSuperHirn OpenSwathMzMLFileCacher OpenSwathRewriteToFeatureXML IDPosteriorErrorProbability IDFileConverter IDScoreSwitcher MapAlignerTreeGuided MapNormalizer MascotAdapter MetaboliteAdductDecharger MRMPairFinder MSstatsConverter MzTabExporter NoiseFilterGaussian NoiseFilterSGolay OpenPepXLLF OpenSwathChromatogramExtractor OpenSwathAnalyzer OpenSwathFileSplitter OpenSwathRTNormalizer PhosphoScoring HighResPrecursorMassCorrector PrecursorMassCorrector QCCalculator CruxAdapter ConsensusMapNormalizer QCImporter SpectraFilterScaler QCShrinker QCExtractor ProteinResolver IDExtractor LowMemPeakPickerHiRes LowMemPeakPickerHiResRandomAccess MT2MQ 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 Pathway Matcher Raw Tools DIA_Umpire_SE CustomProDB QuanTP MALDIquant preprocessing 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 X!Tandem MSMS Search X!Tandem MSMS Search metaMS.runGC Isoplot: Generate plots from isocor output xcms refineChromPeaks (refine) W4m Data Subset Align Samples Replicate Filter Process Scans (and SIM-Stitch) MetFrag Vis OPLS-DA_Contrasts 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 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 Join +/- Ions Generic_Filter Quality Metrics Multilevel Check Format Determine_batch_correction Batch_correction MassBank spectrum searches ProbMetab Tool CAMERA.combinexsAnnos proFIA NMR_Bucketing NMR_Normalization NMR spectra alignment GROMACS copy file Extracting Topology Information alphafold Build tLEaP RDConf: Low-energy ligand conformer search Trajectory select and merge VINA Docking Extract energy components with GROMACS Descriptors Convert Amber topology and coordinate files to GROMACS format GROMACS solvation and adding ions GROMACS simulation GROMACS energy minimization Convert Parameters Generate MD topologies for small molecules Create GROMACS index files Create GROMACS position restraints files Modify/convert GROMACS trajectories Merge GROMACS topologies ParmChk2 AnteChamber MMPBSA/MMGBSA dpocket OpenPepXL fpocket Pharmacophore alignment Pharmacophore Calculate the box parameters using RDKit MDTraj file converter dcTMD friction correction GROMACS production simulation Score docked poses using SuCOS Search ChEMBL database ChEMBL structure pipeline GROMACS structure configuration 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 Slice MD trajectories Drug-likeness Adding New Topology Information Remove protonation state GROMACS Radius of Gyration 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 Calculate molecular descriptors PubChem Download PubChem Assay Downloader Prepare ligand Remove duplicated molecules Filter Compound conversion Visualisation Compute physico-chemical properties Compound search Remove small molecules Prepare ligands for docking Cluster ligands using SuCOS Max SuCOS score Determine distance to defined points Create Frankenstein ligand rDock cavity definition rDock docking rDock docking rxDock cavity definition rxDock docking SDF sort and filter Calculate plane of best fit for molecules Reaction SMARTS filter Generate conformers Constrained conformer generation Butina Cluster Matrix Open 3D Align Standardize SD-files Butina Cluster Pick Reaction maker Screen XCos 'FeatureStein' fragment overlay scoring OpenDUck chunk Run OpenDUck XChem TransFS pose scoring Molecule to fingerprint NxN clustering Taylor-Butina clustering SDF to Fingerprint fastpca Alchemical Analysis goseq Hydrogen Bond Analysis using VMD PCA visualization RMSF Analysis PCA RMSD Analysis DCCM analysis PACKMOL PaDEL descriptor Online data Get PDB file Multi Compound Search Remove counterions and fragments Substructure Search Multi Compound Search Spectrophores(TM) search: Molecule recognition Natural Product Similarity Search Conformer calculation MDS Scatter Plot Online data Fragmenter PubChem Assay Downloader Merging Open Molecule Generator
RGCCA 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 To categorical Machine Learning Visualization Extension LightGBM Split Dataset Fit a Pipeline, Ensemble Stacking Ensembles Estimator attributes Model Prediction Train, Test and Evaluation Model Validation Discriminant Analysis Calculate metrics Feature Selection Numeric Clustering Nearest Neighbors Classification Pipeline Builder Hyperparameter Search Generate Support vector machines (SVMs) Evaluate pairwise distances Ensemble methods Preprocess Calculate metrics Generalized linear models Evaluate a Fitted Model Principal component analysis Deep learning training and evaluation 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 pyGenomeTracks Heatmap w ggplot Violin plot w ggplot2 Scatterplot with ggplot2 Histogram with ggplot2 Circos: Alignments to links Circos: Link Density Track Circos: Bundle Links Circos GC Skew Circos: Resample 1/2D data Circos: bigWig to Scatter Circos: Stack bigWigs as Histogram Circos: Table viewer Circos: Interval to Circos Text Labels Circos: Interval to Tiles Pretext Snapshot Bandage Info Pairwise intersection UpSet diagram Volcano Plot JBrowse - Data Directory to Standalone JBrowse Paired-end histogram Build custom track Scatterplot PCA plot w ggplot2 Histogram GMAJ Plotting tool BAM Coverage Plotter Bandage Image Plot confusion matrix, precision, recall and ROC and AUC curves Newick Display Krona pie chart Pathview Export to GraPhlAn Venn Diagram heatmap2 Plot actual vs predicted curves and residual plots Parallel Coordinates Plot Fasta nucleotide color plot GraPhlAn Generation, personalization and annotation of tree rtsne Visualize with Krona Fasta nucleotide color plot MUMmer dotplot Karyotype Plotting tool Bar chart Boxplot LAJ VCF to MAF Custom Track
codeML IQ-TREE TN93 Cluster TN93 Join neighbors TN93 Filter Mutate Codons Merge matching reads Structure aaChanges phyloP MEME-ChIP Sequence Logo MEME psp-gen FIMO MEME 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 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 map plotting NetCDF xarray Coordinate Info NetCDF xarray Metadata Info NetCDF xarray Selection NetCDF xarray operations 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 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 CDO get info CDO Operations EODIE Copernicus Atmosphere Data Store CESM Copernicus Climate Data Store CTSM/FATES-EMERALD Copernicus Essential Climate Variables climate stripes map plot zonal statistics shift longitudes Retrieve JBrowse GFF3 to Apollo Annotations Retrieve Data Annotate Create or Update Organism Delete an Apollo record Register Account List Organisms Delete all annotations from an Apollo record Local Threshold Auto Threshold Projective Transformation Projective Transformation IDR/OMERO Download Spot Detection Association of points Curve Fitting CellProfiler Starting Modules ColorToGray Tile Image Registration TrackObjects OverlayOutlines ConvertObjectsToImage DisplayDataOnImage EnhanceOrSuppressFeatures ExportToSpreadsheet GrayToColor IdentifyPrimaryObjects MaskImage MeasureGranularity MeasureImageAreaOccupied MeasureImageIntensity MeasureImageQuality MeasureObjectIntensity MeasureObjectSizeShape MeasureTexture RelateObjects SaveImages ImageMath Landmark Registration 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 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 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 Visceral Binary To Points Slice Image Split Labelmap 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 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 UCSC Cell Browser 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 Scanpy ParameterIterator Scanpy PlotTrajectory Scmap index cells 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 DBKit Merge DBKit Extract SPRING Model SPRING Min-Z SPRING Cross PubMed query Text to wordmatrix Get PubMed abstracts PMIDs to PubTator SPRING Model-All SPRING Map SPRING MCC DBKit Create Statistics on presence-absence Variables exploration Local Contributions to Beta Diversity (LCBD) Homoscedasticity and normality Presence-absence and abundance Spatial coordinates anonymization tracy Assemble tracy Basecall tracy Decompose tracy Align