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GenomicFeatures Resource Report Resource Website 50+ mentions	GenomicFeatures (RRID:SCR_016960)		software application, data analysis software, software resource, data processing software, software toolkit	Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.	making, manipulating, transcript, centric, annotation, genomic, location, exon, cds, bio.tools	is used by: riboWaltz is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing	NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635	PMID:23950696	Free, Available for download, Freely available	biotools:genomicfeatures	https://bio.tools/genomicfeatures		SCR_016960		2026-07-28 09:44:30	65
riboWaltz Resource Report Resource Website 10+ mentions	riboWaltz (RRID:SCR_016948)		software application, data analysis software, software resource, data processing software, data visualization software	Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.	calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate	uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing	Autonomous Province of Trento ; Wellcome Trust	PMID:30102689	Free, Available for download, Freely available				SCR_016948		2026-07-28 09:44:26	21
Bioconductor Resource Report Resource Website 10000+ mentions	Bioconductor (RRID:SCR_006442)		software repository, software toolkit, software resource	Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.	catalog, analysis, genomic, metadata, comprehension, statistical, data	lists: MSstats lists: MetaCyto lists: MetaNeighbor lists: tximport lists: clusterProfiler lists: ropls lists: FlowSOM lists: scran lists: Rsubread lists: riboSeqR lists: Biostrings lists: ConsensusClusterPlus lists: DESeq2 lists: GenomicFeatures lists: affy lists: affydata lists: Genomic Ranges lists: Goseq lists: GAGE lists: CATALYST lists: Scmap lists: Scfind lists: GenomicRanges lists: org.Rn.eg.db lists: Extending Guilt by Association by Degree lists: ggtree lists: StructuralVariantAnnotation lists: scTHI lists: EnhancedVolcano lists: DEGreport lists: variancePartition lists: biomaRt lists: MSnbase lists: ReactomePA lists: SynergyFinder lists: CiteFuse lists: fgsea lists: GSVA lists: SimFFPE lists: FilterFFPE lists: PhenStat lists: ChIPseeker lists: AUCell lists: svaNUMT lists: KEGGgraph lists: epialleleR lists: microbiome lists: Orthology.eg.db lists: org.Hs.eg.db lists: ExperimentHub lists: combi is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: SoftCite is affiliated with: RnaSeqGeneEdgeRQL is related to: asSeq is related to: Gene Ontology is related to: CRCView is related to: R Project for Statistical Computing is related to: GEO2R is related to: LIMMA is related to: VisR is related to: edgeR is related to: IMEx - The International Molecular Exchange Consortium is related to: CATALYSTLite is related to: ascend is related to: minet has parent organization: Fred Hutchinson Cancer Center is parent organization of: ncdfFlow is parent organization of: GenomicRanges is parent organization of: ReadqPCR is parent organization of: flowCL is parent organization of: flowBin is parent organization of: CorMut is parent organization of: metaSeq is parent organization of: VariantAnnotation is parent organization of: ReQON is parent organization of: timecourse is parent organization of: RmiR.Hs.miRNA is parent organization of: AffyRNADegradation is parent organization of: ArrayExpress (R) is parent organization of: GEOquery is parent organization of: MIMOSA is parent organization of: HEM is parent organization of: CNTools is parent organization of: cn.FARMS is parent organization of: Clonality is parent organization of: TransView is parent organization of: pvac is parent organization of: QUALIFIER is parent organization of: flowStats is parent organization of: rTANDEM is parent organization of: flowFlowJo is parent organization of: iASeq is parent organization of: OLINgui is parent organization of: SigFuge is parent organization of: Rdisop is parent organization of: GeneExpressionSignature is parent organization of: iBMQ is parent organization of: TDARACNE is parent organization of: flowQ is parent organization of: FlipFlop is parent organization of: RmiR is parent organization of: bsseq is parent organization of: ExomePeak is parent organization of: flowWorkspace is parent organization of: massiR is parent organization of: rbsurv is parent organization of: GeneMeta is parent organization of: MergeMaid is parent organization of: categoryCompare is parent organization of: metahdep is parent organization of: snpStats: SnpMatrix and XSnpMatrix classes and methods is parent organization of: CNVtools is parent organization of: CGEN is parent organization of: RCASPAR is parent organization of: iterativeBMAsurv is parent organization of: multtest is parent organization of: globaltest is parent organization of: MinimumDistance is parent organization of: VegaMC is parent organization of: VanillaICE is parent organization of: SNPchip is parent organization of: SMAP is parent organization of: quantsmooth is parent organization of: mBPCR is parent organization of: ITALICS is parent organization of: GenoSet is parent organization of: exomeCopy is parent organization of: CGHregions is parent organization of: CGHbase is parent organization of: beadarraySNP is parent organization of: GLAD is parent organization of: methylMnM is parent organization of: methyAnalysis is parent organization of: ARRmNormalization is parent organization of: ChIPsim is parent organization of: yaqcaffy is parent organization of: wateRmelon is parent organization of: sRAP is parent organization of: spotSegmentation is parent organization of: SNM is parent organization of: SNAGEE is parent organization of: Simpleaffy is parent organization of: qcmetrics is parent organization of: MANOR is parent organization of: limmaGUI is parent organization of: ffpe is parent organization of: dyebias is parent organization of: DEXUS is parent organization of: BeadDataPackR is parent organization of: aroma.light is parent organization of: ArrayTools is parent organization of: beadarray is parent organization of: arrayQuality is parent organization of: arrayMvout is parent organization of: affyQCReport is parent organization of: affyPLM is parent organization of: AffyExpress is parent organization of: waveTiling is parent organization of: gprege is parent organization of: oneChannelGUI is parent organization of: LMGene is parent organization of: factDesign is parent organization of: pickgene is parent organization of: betr is parent organization of: SCAN.UPC is parent organization of: arrayQualityMetrics is parent organization of: CALIB is parent organization of: DEDS is parent organization of: Harshlight is parent organization of: MiChip is parent organization of: OCplus is parent organization of: bridge is parent organization of: fRMA is parent organization of: genArise is parent organization of: lapmix is parent organization of: maCorrPlot is parent organization of: maSigPro is parent organization of: MACAT is parent organization of: maigesPack is parent organization of: MDQC is parent organization of: metaArray is parent organization of: nnNorm is parent organization of: plgem is parent organization of: PVCA is parent organization of: RAMA is parent organization of: stepNorm is parent organization of: virtualArray is parent organization of: LPE is parent organization of: vsn is parent organization of: ACME is parent organization of: CoGAPS is parent organization of: flowFP is parent organization of: rMAT is parent organization of: SLqPCR is parent organization of: nondetects is parent organization of: unifiedWMWqPCR is parent organization of: sSeq is parent organization of: CNVrd2 is parent organization of: plateCore is parent organization of: RSVSim is parent organization of: TCC is parent organization of: CQN is parent organization of: COMPASS is parent organization of: flowClust is parent organization of: SPADE is parent organization of: OrderedList is parent organization of: SamSPECTRAL is parent organization of: flowUtils is parent organization of: RchyOptimyx is parent organization of: TEQC is parent organization of: flowType is parent organization of: ADaCGH2 is parent organization of: flowViz is parent organization of: flowTrans is parent organization of: flowQB is parent organization of: shinyTANDEM is parent organization of: flowPlots is parent organization of: flowPhyto is parent organization of: flowCore is parent organization of: flowMerge is parent organization of: flowMap is parent organization of: flowMeans is parent organization of: spliceR is parent organization of: flowMatch is parent organization of: flowFit is parent organization of: flowCyBar is parent organization of: BEAT is parent organization of: flowBeads is parent organization of: CAMERA - Collection of annotation related methods for mass spectrometry data is parent organization of: MBASED is parent organization of: MethylAid is parent organization of: sapFinder is parent organization of: Pathview is parent organization of: DSS is parent organization of: RMassBank is parent organization of: iontree is parent organization of: Basic4Cseq is parent organization of: BiGGR is parent organization of: mzR is parent organization of: PAPi is parent organization of: CGHnormaliter is parent organization of: Chimera is parent organization of: BRAIN is parent organization of: tweeDEseq is parent organization of: SurvComp is parent organization of: Triplex is parent organization of: OmicCircos is parent organization of: ggbio is parent organization of: HTqPCR is parent organization of: NormqPCR is parent organization of: ddCt is parent organization of: EasyqpcR is parent organization of: SWAN is parent organization of: PING is parent organization of: DMRforPairs is parent organization of: SeqGSEA is parent organization of: h5vc is parent organization of: deepSNV is parent organization of: RUVSeq is parent organization of: BHC is parent organization of: epigenomix is parent organization of: IRanges is parent organization of: GeneNetworkBuilder is parent organization of: MethylSeekR is parent organization of: SRAdb is parent organization of: casper is parent organization of: htSeqTools is parent organization of: ChIPXpress is parent organization of: methVisual is parent organization of: DeconRNASeq is parent organization of: EDASeq is parent organization of: RIPSeeker is parent organization of: ShortRead is parent organization of: seqbias is parent organization of: DEGseq is parent organization of: arrayMagic is parent organization of: easyRNASeq is parent organization of: DNAcopy is parent organization of: CRLMM is parent organization of: motifRG is parent organization of: MMDiff is parent organization of: MiRaGE is parent organization of: LVSmiRNA is parent organization of: ExiMiR is parent organization of: RPA is parent organization of: CexoR is parent organization of: lumi is parent organization of: baySeq is parent organization of: tRanslatome is parent organization of: DNaseR is parent organization of: DEXSeq is parent organization of: ChIPpeakAnno is parent organization of: inSilicoMerging is parent organization of: minfi is parent organization of: Methylumi is parent organization of: miRNApath is parent organization of: sva package is parent organization of: dmrFinder is parent organization of: rqubic is parent organization of: BicARE is parent organization of: iBBiG is parent organization of: eisa is parent organization of: ChAMP is parent organization of: cghMCR is parent organization of: Bioconductor mailing list is parent organization of: DiffBind is parent organization of: NarrowPeaks is parent organization of: CSAR is parent organization of: CSSP is parent organization of: TargetScore is parent organization of: snapCGH is parent organization of: iChip is parent organization of: TurboNorm is parent organization of: Ringo is parent organization of: RLMM is parent organization of: charm is parent organization of: BiSeq is parent organization of: MEDME is parent organization of: MEDIPS is parent organization of: BayesPeak is parent organization of: ChIPseqR is parent organization of: Rolexa is parent organization of: cn.mops is parent organization of: RankProd is parent organization of: phyloseq is parent organization of: HiTC is parent organization of: CancerMutationAnalysis is parent organization of: aCGH is parent organization of: Repitools is parent organization of: flowPeaks is parent organization of: Mfuzz is parent organization of: les is parent organization of: OLIN is parent organization of: affylmGUI is parent organization of: CYCLE is parent organization of: r3Cseq is parent organization of: Piano is parent organization of: RamiGO hosts: DESeq hosts: rGADEM hosts: PICS hosts: Jmosaics hosts: R453Plus1Toolbox hosts: BAC hosts: targetscan.Hs.eg.db hosts: Starr hosts: Qvalue hosts: topGO hosts: MmPalateMiRNA hosts: CGHcall hosts: EGSEA hosts: NOISeq	Catt Family Foundation ; Dana Farber Cancer Institute ; NHGRI R33 HG002708	PMID:15461798	Free, Freely available	OMICS_01759, nif-0000-10445			SCR_006442		2026-07-28 09:41:34	22974
R Project for Statistical Computing Resource Report Resource Website 10000+ mentions	R Project for Statistical Computing (RRID:SCR_001905)	R	software resource	Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.	R software, statistical, computing, graphics, programming, language, bio.tools	is used by: UTR is used by: MSstats is used by: CummeRbund is used by: deFuse is used by: JASP is used by: Boruta is used by: NMRProcFlow is used by: PlotsOfData is used by: rtransparent is used by: shinyCircoss is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: CRAN is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is related to: Sweave is related to: rOpenSci is related to: R Manuals is related to: Bioconductor is related to: ggplot2 is related to: madsim is related to: Solas is related to: braincog is related to: clustree is related to: PhenoSpD is related to: geomorph is related to: NeuroAnatomy Toolbox is related to: dplyr is related to: glmmADMB is related to: clusterProfiler is related to: ropls is related to: mixOmics is related to: FlowSOM is related to: Rtsne is related to: scran is related to: Rsubread is related to: riboSeqR is related to: Biostrings is related to: riboWaltz is related to: GenomicFeatures is related to: devtools is related to: affy is related to: affydata is related to: Heatmapper is related to: toxprofileR is related to: LTRpred is related to: RaceID is related to: PRSice is related to: Genomic Ranges is related to: Goseq is related to: GAGE is related to: metagear is related to: pagoda2 is related to: dndSCV is related to: tidyr is related to: ClustVis is related to: IDR is related to: NeuroAnatomy Toolbox is related to: rjags is related to: gProfiler2 is related to: knitr is related to: EpiEstim is related to: Minimum-Hypergeometric Test is related to: Network-Based R-Statistics is related to: seqpac is related to: survminer is related to: Vector Generalized Linear and Additive Models is related to: LEA is related to: StAMPP is related to: Betareg is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: Rphenograph is related to: Peptides is related to: taxize is related to: seqinr is related to: reshape2 is related to: monaLisa is related to: mia is related to: Rtsne is related to: R package:stats-package is related to: R package: maxstat is related to: stats		PMID:18252159		SCR_021974, nif-0000-10474, OMICS_01147, biotools:r	https://cran.r-project.org/src/base/R-3/, https://bio.tools/r		SCR_001905	R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing	2026-07-25 12:05:16	47818
bio.tools Resource Report Resource Website 10+ mentions	bio.tools (RRID:SCR_014695)		data or information resource, catalog, database, software resource, software repository	Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.	Registry, software registry, biological tool, data services registry, services discovery portal, bio.tools	lists: FACS lists: Fusion Analyser lists: AffyRNADegradation lists: GUARDD lists: GEOquery lists: RNAcontext lists: Patchwork lists: SODOCK lists: MIMOSA lists: GraBCas lists: SNAVI lists: GENIE3 lists: Megraft lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: PeptideProphet lists: Quant lists: VARiD lists: ProteinProphet lists: Flicker lists: ARACHNE lists: Micro-Analyzer lists: riboPicker lists: dbSTS lists: POPBAM lists: flowPeaks lists: cn.FARMS lists: Sequence Search and Alignment by Hashing Algorithm lists: SAMBLASTER lists: Pindel lists: Mfuzz lists: TAPyR lists: ContEst lists: PGS lists: PEPPER lists: FPSAC lists: FlipFlop lists: ProGlycProt lists: MuTect lists: TriageTools lists: BLASR lists: DSRC lists: SRMA lists: Bowtie lists: StringTie lists: PhenoFam lists: SOAP lists: SplitSeek lists: MUSCLE lists: SplicePlot lists: Illuminator lists: GimmeMotifs lists: Skylign lists: BreakSeq lists: Barrnap lists: SLOPE lists: CUDA-EC lists: QualiMap lists: massiR lists: OmicsOffice for NGS SeqSolve lists: QUAST lists: GenomicTools lists: NGSUtils lists: TileQC lists: Sequedex lists: PARalyzer lists: BFCounter lists: TALLYMER lists: SNPchip lists: VAAL lists: ProbRNA lists: ADMIXTURE lists: SABER lists: piCALL lists: CYCLE lists: limmaGUI lists: DEXUS lists: KAnalyze lists: BeadDataPackR lists: wateRmelon lists: NGSrich lists: OLIN lists: fRMA lists: MACAT lists: affylmGUI lists: DictyOGlyc lists: GlyProt lists: CisGenome lists: ToppCluster lists: AnimalTFDB lists: oneChannelGUI lists: YinOYang lists: Chilibot: Gene and Protein relationships from MEDLINE lists: asSeq lists: FARMS lists: GERMLINE lists: unifiedWMWqPCR lists: HAPLOPAINTER lists: Biocatalogue - The Life Science Web Services Registry lists: HOMOZYGOSITYMAPPER lists: MetaBase lists: PyLOH lists: InterMine lists: myExperiment lists: pRESTO lists: TANGO lists: Prediction of Amyloid Structure Aggregation lists: PhosphoSitePlus: Protein Modification Site lists: CCAT lists: BREAKDANCER lists: FACTA+. lists: PEDIGRAPH lists: CQN lists: CanSNPer lists: SamSPECTRAL lists: TEMP lists: MEME Suite - Motif-based sequence analysis tools lists: SNPAAMapper lists: Pecan lists: InteroPorc lists: AffyPipe lists: ADaCGH2 lists: DINDEL lists: ASPGD lists: Candida Genome Database lists: BISC lists: PurBayes lists: SNVer lists: Cake lists: S-MART lists: SHORTY lists: Pathway Commons lists: TcoF lists: BEETL-fastq lists: SBARS lists: cpnDB: A Chaperonin Database lists: cisRED: cis-regulatory element lists: FlyFactorSurvey lists: pymzML lists: EchoBASE lists: Blood Group Antigen Gene Mutation Database lists: WebGeSTer DB lists: RUbioSeq lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: MethylAid lists: ExomeDepth lists: ZOOM lists: Iterative Signature Algorithm lists: ShotGun lists: Pathview lists: T3DB lists: Autophagy Database lists: rBiopaxParser lists: QualitySNPng lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: libCSAM lists: RopeBWT2 lists: NetPathMiner lists: BioNumbers lists: leeHom lists: tweeDEseq lists: ProRata lists: Coding Potential Calculator lists: CPTRA lists: MFEprimer lists: Distant Regulatory Elements lists: HGNC lists: GATE lists: SuperPred: Drug classification and target prediction lists: hot scan lists: AltAnalyze - Alternative Splicing Analysis Tool lists: Primer3Plus lists: pairheatmap lists: BioJS lists: ms lims lists: Eukaryotic Linear Motif lists: Proteome Analyst Specialized Subcellular Localization Server lists: HYDEN lists: drFAST lists: GeneFisher lists: GreenPhylDB lists: MiST - Microbial Signal Transduction database lists: Pipeliner lists: Gene Set Enrichment Analysis lists: Piano lists: Weighted Gene Co-expression Network Analysis lists: FastSNP lists: Triplex lists: mrsFAST lists: GenePattern lists: NovelSeq lists: QDNAseq lists: MutDB lists: SplicingCompass lists: deFuse lists: Database of Interacting Proteins (DIP) lists: Assembly Based ReAligner lists: MAGE-TAB lists: ggbio lists: miR-PREFeR lists: NanoStringNorm lists: MIPgen lists: HTqPCR lists: Parseq lists: T-profiler lists: Bpipe lists: jmzTab lists: L-Measure lists: Snakemake lists: PoPoolation lists: MultiPhen lists: PheWAS R Package lists: Quantitative Enrichment of Sequence Tags lists: ALDEx2 lists: INMEX lists: InsertionMapper lists: BSRD lists: SeWeR - SEquence analysis using WEb Resources lists: Segway - a way to segment the genome lists: Stem Cell Discovery Engine lists: TagDust lists: Kdetrees lists: Tree and reticulogram REConstruction lists: NEWT lists: DER Finder lists: BioPig lists: Selectome: a Database of Positive Selection lists: Distributed String Mining Framework lists: PILGRM lists: Apo and Holo structures DataBase lists: MLTreeMap lists: MG-RAST lists: miRNAKey lists: SVseq lists: Small Molecule Pathway Database lists: Information Hyperlinked Over Proteins lists: SVMerge lists: BioSample Database at EBI lists: MetaPhyler lists: SOPRA lists: NCBI BioSystems Database lists: SLIQ lists: G-BLASTN lists: SSPACE lists: AmphoraNet lists: NCBI Structure: Cn3D lists: DELLY lists: RUM lists: STING Report lists: SoyBase lists: SINA lists: Strelka2 lists: RNA-eXpress lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets lists: VFS lists: ShoRAH lists: READSCAN lists: ERANGE lists: GeneTalk lists: ORMAN lists: SEECER lists: Scripture lists: SPOT - Biological prioritization after a SNP association study lists: NCBO Annotator lists: CoPub lists: SolexaQA lists: PHAge Search Tool lists: Knime4Bio lists: MethPipe lists: Bis-SNP lists: GobyWeb lists: EMAGE Gene Expression Database lists: FusionMap lists: Yabi lists: GSNAP lists: rQuant lists: MethylViewer lists: DistMap lists: PASS lists: mrFAST lists: Kismeth lists: Stampy lists: TreQ lists: FLASH lists: SAMStat lists: PRINSEQ lists: MethylomeDB lists: SOAPaligner/soap2 lists: TMA Navigator lists: TRANSFAC lists: SeqMap lists: Bambino lists: MicrobesOnline lists: DMRforPairs lists: TIGRFAMS lists: CLIPZ lists: SNPsandGO lists: ToppGene Suite lists: SeqTrace lists: GoSurfer lists: Jellyfish lists: GoFish lists: WEGO - Web Gene Ontology Annotation Plot lists: ngsTools lists: GraphProt lists: SerbGO lists: GoPubMed lists: ccPDB - Compilation and Creation of datasets from PDB lists: DOMMINO - Database Of MacroMolecular INteractiOns lists: SOURCE lists: DistiLD - Diseases and Traits in LD lists: PePr lists: Expression Profiler lists: eQuilibrator lists: DiseaseMeth lists: Dr.VIS - Human Disease-Related Viral Integration Sites lists: FunTree lists: DBETH - Database for Bacterial ExoToxins for Humans lists: BLESS lists: GWASdb lists: HFV Database lists: IndelFR - Indel Flanking Region Database lists: MIPModDB lists: Europe PubMed Central lists: CharProtDB: Characterized Protein Database lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature lists: MMMDB - Mouse Multiple tissue Metabolome DataBase lists: ICEberg lists: VirHostNet: Virus-Host Network lists: Cascade lists: Polbase lists: VIRsiRNAdb lists: 959 Nematode Genomes lists: OGEE - Online GEne Essentiality database lists: ProPortal lists: SNPedia lists: Newtomics lists: HotRegion - A Database of Cooperative Hotspots lists: SitEx lists: ScerTF lists: HMM-TM lists: NRG-CING lists: PRED-LIPO lists: InterEvol database lists: SpliceDisease lists: RNA CoSSMos lists: deepSNV lists: PRED-GPCR lists: RecountDB lists: VICUNA lists: ProRepeat lists: MouseBook lists: COEUS lists: Predictive Networks lists: PRED-SIGNAL lists: Flycircuit lists: COLT-Cancer lists: ATRHUNTER lists: GeneTrail lists: epigenomix lists: Pseudomonas Genome Database lists: QCGWAS lists: TSSer lists: UMD-BRCA1/ BRCA2 databases lists: PomBase lists: Phytozome lists: OMPdb lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: MSIsensor lists: GWAMA lists: SpliceTrap lists: ViralZone lists: waviCGH lists: MyHits lists: Decombinator lists: CAPS Database lists: ADGO lists: zfishbook lists: EagleView lists: Gene Expression Database lists: SRAdb lists: BEDTools lists: IMGT/GENE-DB lists: RamiGO lists: canSAR lists: IMGT/LIGM-DB lists: PLEXdb - Plant Expression Database lists: COHCAP lists: DARC - Database for Aligned Ribosomal Complexes lists: Immune Epitope Database and Analysis Resource (IEDB) lists: AutismKB lists: RIKEN integrated database of mammals lists: Myrna lists: PhenoM - Phenomics of yeast Mutants lists: BIGpre lists: HIstome: The Histone Infobase lists: TriTrypDB lists: CuticleDB lists: Midbody, Centrosome and Kinetochore lists: SCOP: Structural Classification of Proteins lists: Expression Database in 4D lists: VIDA lists: Database of Arabidopsis Transcription Factors lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology lists: ESEfinder 3.0 lists: agriGO lists: Taipan lists: AgBase lists: Chromosome 7 Annotation Project lists: MEROPS lists: T1DBase lists: Hyper Cell Line Database lists: GenoTan lists: VISTA Browser lists: lobSTR lists: Candidate Genes to Inherited Diseases lists: VISTA Enhancer Browser lists: Gene Array Analyzer lists: Network Analysis, Visualization and Graphing TORonto lists: MuSiC lists: MfunGD - MIPS Mouse Functional Genome Database lists: eTBlast lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) lists: FGDP lists: hiPathDB - human integrated Pathway DB with facile visualization lists: miRNEST lists: neXtProt lists: NetOGlyc lists: QuasiRecomb lists: GMAP lists: iMir lists: MaCH-Admix lists: SeqBuster lists: LegumeIP lists: DNAtraffic lists: MicroSNiPer lists: Pathema lists: BeeBase lists: Geneious lists: MOSCPHASER lists: SNPinfo Web Server lists: elastix lists: MIRA lists: NEBcutter lists: CopySeq lists: CUPSAT lists: Atlas2 lists: ALLPATHS-LG lists: Velvet lists: HomSI lists: SVDetect lists: omiRas lists: HMCan lists: HapFABIA lists: WEBLOGO lists: ZINBA lists: SICER lists: kmer-SVM lists: MAnorm lists: Pedimap lists: nucleR lists: CEQer lists: MutSig lists: DIANA-LncBase lists: MethMarker lists: PeakRanger lists: PlnTFDB lists: CloudBurst lists: NPS lists: MutationTaster lists: ProDesign lists: OligoArray lists: ArrayAnalysis.org lists: PatMaN lists: SEAL lists: Asterias lists: RACE lists: RobiNA lists: CANGS lists: PlantTFcat lists: LitInspector lists: HSLPred lists: PSAR-Align lists: CancerResource lists: JiffyNet lists: ECHO lists: GPU-Meta-Storms lists: GenoREAD lists: TopHat-Fusion lists: GeneStitch lists: FABIA lists: CPFP lists: MFPaQ lists: ICPL ESIQuant lists: easyRNASeq lists: PREDDIMER lists: NetCoffee lists: SlideSort-BPR lists: miRPlant lists: AlienTrimmer lists: PRIDE Converter 2 lists: SNP ratio test lists: compomics-utilities lists: Allim lists: PLEK lists: ISDTool lists: OBI-Warp lists: LocalAli lists: iceLogo lists: multiplierz lists: AMS lists: NGSmethDB lists: PoolHap lists: DNaseR lists: Btrim lists: COBRApy lists: NAIL lists: CAZy- Carbohydrate Active Enzyme lists: A5-miseq lists: ANNOVAR lists: GENSCAN lists: PhosphoSiteAnalyzer lists: MethylCoder lists: featureCounts lists: LOCAS lists: Scalpel lists: Cell motility lists: Mouse Genome Database lists: CloudAligner lists: HeurAA lists: GSA-SNP lists: seqMINER lists: PolyPhen: Polymorphism Phenotyping lists: rqubic lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase lists: MitoBreak lists: Cube-DB lists: Death Domain database lists: Telescoper lists: Crossbow lists: MToolBox lists: GENE-counter lists: BEADS lists: PLAN2L lists: INCLUSive lists: CSAR lists: ApiDB CryptoDB lists: MACS lists: NNcon lists: KAVIAR lists: GeneSigDB lists: psRNATarget lists: Composition Profiler lists: MINAS - Metal Ions in Nucleic AcidS lists: EGSEA lists: Crystallography and NMR System (CNS) lists: Morpheus lists: IUPHAR/BPS Guide to Pharmacology lists: RAST Server lists: ProteomicsDB lists: SPEX2 lists: LTR_Finder lists: SCRATCH lists: DSAP lists: PALEOMIX lists: Buccaneer lists: QuantiSNP lists: ProtTest lists: MultiQC lists: GeneWise lists: DISEASES lists: Off-Spotter lists: oligo lists: 3D-footprint lists: SC3 lists: MS-GF+ lists: TISSUES lists: TFBS lists: CHiCAGO lists: Poretools lists: Membrane Protein Explorer lists: FATCAT lists: Bio-tradis lists: ALTER lists: HISAT2 lists: MetaMapR lists: PhyD3 lists: Exonerate lists: primers4clades lists: Fastml lists: Bamtools lists: Genesis lists: DISULFIND lists: EnrichmentMap lists: LoRDEC lists: mentha lists: IDEPI - IDentify EPItopes lists: Oufti lists: FluxModeCalculator lists: eXpression2Kinases lists: SMAGEXP lists: ProCon - PROteomics CONversion lists: Lifebit Deploit lists: TRANSIT lists: Splicing Express lists: Microscopy Image Browser lists: SARTools lists: SPICE lists: DINIES lists: OmicsNet lists: ngsRelate lists: clusterProfiler lists: NetworkAnalyst lists: FRETBursts lists: Thunder STORM lists: ANOCVA lists: ConsensusClusterPlus lists: CIBERSORT lists: CCTOP lists: scran lists: Rsubread lists: Heatmapper lists: BinPacker lists: Subread lists: UMI-tools lists: Goseq lists: PRSice lists: ScaffMatch lists: EMBOSSMatcher lists: JAMM lists: CentroidFold lists: Gigwa lists: FastProject lists: GeSeq lists: ComplexHeatmap lists: PatchDock lists: Proovread lists: trimAl lists: ExPASy ABCD database lists: shinyGEO lists: AmoebaDB lists: Blood Exposome Database lists: STRUCTURE lists: NetPhos lists: Geneshot lists: ProtParam Tool lists: HiC-Pro lists: HingeProt lists: Mousebytes lists: iTOL lists: ChiCMaxima lists: SWISS-MODEL lists: PASTEClassifier lists: R/qtl2 lists: FlowCal lists: Signaling Pathways Project lists: GPS-SUMO lists: Roary lists: SpydrPick lists: ProSA-web lists: SIGNOR lists: MaxAlign lists: REDIportal lists: EpiModel lists: Protein Interactions Calculator lists: rVista lists: Minimap2 lists: PrognoScan lists: Batch Web CD-Search Tool lists: AlgPred lists: GOnet lists: GalaxyWEB lists: GalaxyRefine lists: Annotree lists: khmer lists: E-CRISP lists: Robetta lists: D-GENIES lists: aroma.light lists: Clustal Omega lists: DESeq lists: VICMpred lists: Ray lists: Apollo lists: STAMP lists: discoSnp lists: vcflib lists: IgBLAST lists: BioPerl lists: Genome BioInformatics Research Lab - gff2ps lists: Rainbow lists: Predictions for Entire Proteomes lists: Stacks lists: Clustal W2 lists: RNAhybrid lists: Primer3 lists: SAMtools/BCFtools lists: EBSeq lists: biobambam lists: DIALIGN lists: Unipro UGENE lists: Bowtie 2 lists: Artemis: Genome Browser and Annotation Tool lists: WHAM lists: Database of Secondary Structure Assignments lists: Minia lists: HTSeq lists: RAxML lists: Sickle lists: Segemehl lists: Staden Package lists: Bismark lists: NCBI BLAST lists: Vienna RNA lists: GBrowse lists: ea-utils lists: AmpliconNoise lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: BitSeq lists: HilbertVis lists: VarScan lists: Regulatory Sequence Analysis Tools lists: CD-HIT lists: MACH lists: SOAPsnp lists: ProbCons lists: BEAST lists: Crux tandem mass spectrometry analysis software lists: Pscan-ChIP lists: BRIG lists: tRNAscan-SE lists: CGView lists: Circos lists: FreeBayes lists: Glimmer lists: T-Coffee lists: Oases lists: LIMMA lists: cutadapt lists: SSAKE lists: edgeR lists: OpenMS lists: Flexbar lists: SIFT lists: Mauve lists: Kalign lists: RSEM lists: TopHat lists: DNAcopy lists: phyloseq lists: Trinity lists: AMOS lists: FastTree lists: Cufflinks lists: Prokka lists: PAML lists: CummeRbund lists: GROMACS lists: minet lists: Atac lists: Pilon lists: GMA lists: Nanopolish lists: Krona lists: SeqPrep lists: SortMeRNA lists: THESIAS lists: tximport lists: StoatyDive lists: rCASC lists: precrec lists: IMGT-ONTOLOGY lists: KAT lists: globaltest lists: COPASI lists: CheckM lists: Blobtools lists: NiftyPET lists: SeaView lists: ASHLAR lists: KisSplice lists: metagen lists: BUSCO lists: BLINK lists: bridge lists: Fcirc lists: becas lists: bwtool lists: TGS-GapCloser lists: chimerascan lists: GLUE lists: mosdepth lists: dcmqi lists: SwiftOrtho lists: andi lists: metahdep lists: HaploReg lists: Jalview lists: ScanITD lists: ImaGene lists: BioNix lists: qrqc lists: MeroX lists: sleuth lists: imDEV lists: MiXCR lists: mlgt lists: SMARTdenovo lists: casper lists: miRDB lists: shovill lists: NiftyFit lists: libmgf lists: rbsurv lists: HH-suite lists: affy lists: StatAlign lists: quantsmooth lists: Fiji lists: yaqcaffy lists: Racon lists: h5vc lists: seqbias lists: tensorflow lists: MGnify lists: ngs.plot lists: dyebias lists: Eoulsan lists: Cuffdiff lists: bsseq lists: VEnCode lists: OrthoFinder lists: genomation lists: SymPy lists: eTRIKS lists: ascat lists: Bridger lists: GADMA lists: lumi lists: PIRATE lists: Hippocampome.org lists: HaTSPiL lists: XL-mHG lists: VETA lists: mitopred lists: ropls lists: sabre lists: scanpy lists: icy lists: plgem lists: MethBase lists: biobakery lists: minfi lists: HyPhy lists: MyGene.info lists: EpiEstim lists: NanoSim lists: fracridge lists: TDimpute lists: Pavian lists: SimVascular lists: qcmetrics lists: Laniakea lists: CRISPRcasIdentifier lists: BISE lists: ODAM lists: MRIcron lists: smashpp lists: BSA4Yeast lists: neuroelectro lists: RepeatFiller lists: ShinyLearner lists: docker4seq lists: CRISPR-ERA lists: MAFFT lists: RepeatScout lists: Phenoscape lists: PhenoMeNal lists: multtest lists: TransDecoder lists: les lists: PlotTwist lists: CRISPR-P lists: Telescope lists: charm lists: Warp lists: skewer lists: Human Neocortical Neurosolver lists: ggtree lists: Datanator lists: genehunter-imprinting lists: GraphClust2 lists: eisa lists: scVelo lists: GEMINI lists: beadarray lists: NGSEP lists: ProP Server lists: CandiMeth lists: METAREP lists: scater lists: BioBERT lists: iontree lists: MetaP lists: larvalign lists: UALCAN lists: VAPPER lists: halSynteny lists: EvidenceFinder lists: bcbio-nextgen lists: QuickNII lists: QIIME lists: phantompeakqualtools lists: MCScan lists: pepwheel lists: PathwayMatcher lists: vsn lists: VisR lists: Galaxy scater lists: OpenWorm lists: ffpe lists: timecourse lists: Metascape lists: Bio2BEL lists: RDXplorer lists: ActiveDriver lists: GENCODE lists: CRISPRdirect lists: GeneMarkS-T lists: SPM lists: Bionitio lists: ascend lists: TCW lists: NanoPipe lists: NeuroChaT lists: pheatmap lists: prank lists: Online Peri-Event Time Histogram for Open Ephys lists: kallisto lists: ggplot2 lists: odMLtables lists: glycomedb lists: pickgene lists: GigaSOM.jl lists: pvac lists: EHRtemporalVariability lists: GemSIM lists: lapmix lists: PAFScaff lists: refgenie lists: biospytial lists: EnteroBase lists: QGIS lists: CLIP-Explorer lists: RatMine lists: NMRProcFlow lists: cn.mops lists: SPP lists: seq-annot lists: PsyGeNET lists: PASA lists: UniCarb-DB lists: NormqPCR lists: PhylomeDB lists: SnpHub lists: ReadqPCR lists: circlize lists: HmtVar lists: sim4cc lists: gprege lists: FusionCatcher lists: UniCarbKB lists: clustergrammer lists: clipcrop lists: metabnorm lists: rnaQUAST lists: VirusMINT lists: breseq lists: PerM lists: SnpEff lists: DecGPU lists: e-Driver lists: NCBI BioProject lists: Flye lists: nondetects lists: PEMer lists: VCFtools lists: STAR lists: fastqz lists: SAMTOOLS lists: Neuroscience Information Framework lists: eProbalign lists: dbEST lists: Dali Server lists: Genomic Ranges lists: GenomicFeatures lists: Cistrome lists: SOAPdenovo lists: IRanges lists: BpForms lists: BcForms lists: DIANA-mirPath lists: AthaMap lists: Ancestrymap lists: AutoDock lists: European Genome phenome Archive lists: GEN3VA lists: 4See lists: ABNER lists: Addgene lists: A Classification of Mobile genetic Elements lists: ADMIXTOOLS lists: AETIONOMY lists: ADMIXMAP lists: ALCHEMY lists: Allele Frequencies in Worldwide Populations lists: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters lists: Alta-Cyclic lists: Alternate splicing gallery lists: Assisted Model Building with Energy Refinement (AMBER) lists: ALOHOMORA lists: AmpliconTagger lists: Molecular Dynamics Workflow (BioKepler) lists: ANDES lists: ALBERT lists: ape lists: ArrayPipe lists: ArrayMiner lists: Aroma.affymetrix lists: ASPEX lists: The Alternatve Splicing Database lists: ASSOCIATIONVIEWER lists: Avogadro lists: AutoAssemblyD lists: BadMedicine lists: BamView lists: BAIT lists: BatMeth lists: AutoDock Vina lists: BARS lists: BCBtoolkit lists: Athena lists: BarraCUDA lists: betaVAEImputation lists: BiG-SLiCE lists: BBSeq lists: SVM based method for predicting beta hairpin structures in proteins lists: BioCarta Pathways lists: BayesEpiModels lists: BiNGO: A Biological Networks Gene Ontology tool lists: BeetleBase lists: BAR lists: BioConda lists: Bioinformatics Toolkit lists: Bionimbus lists: biomaRt lists: Bio++ lists: naiveBayesCall lists: BioSimulations lists: BioPlex lists: Biopieces lists: BRAIN lists: BLAT lists: BS Seeker lists: Breakpointer lists: Canu lists: BioSimulators lists: BRB-ArrayTools lists: bioSyntax lists: CATALYST lists: BOMP: beta-barrel Outer Membrane protein Predictor lists: bioRxiv lists: CAT lists: CCREL lists: BWA lists: CASPAR lists: CARD lists: CATH: Protein Structure Classification lists: CATdb: a Complete Arabidopsis Transcriptome database lists: Cell Image Library (CIL) lists: CEM lists: Cancer Genome Anatomy Project lists: Centrifuge Classifier lists: Bs-Seeker2 lists: ChimeraSlayer lists: ChemSpider lists: BSVF lists: CiLiQuant lists: Chipster lists: CleanEx lists: CHEBI lists: cisTEM lists: CiteFuse lists: clustLasso lists: Chromas lists: ChiRA lists: CNVer lists: CITE-seq-Count lists: CNV-seq lists: circlncRNAnet lists: CMap lists: COGEME Phytopathogenic Fungi and Oomycete EST Database lists: ClinVar lists: ChIPMunk lists: CODEHOP lists: ClustVis lists: CoCo lists: CONTRA lists: Comparative Metatranscriptomics Workflow lists: ComiR lists: CopyDetective lists: ConDeTri lists: Clinotator lists: cortex lists: ClinTrajAn lists: CorMut lists: Coot lists: CRCView lists: CUDASW++ lists: CovalentDock Cloud lists: Chromosome Scale Assembler lists: CYANA lists: Datasets2Tools lists: DBTSS: Database of Transcriptional Start Sites lists: CoryneRegNet lists: CSDeconv lists: CRISPy-web lists: dbSNP lists: ΔG prediction server lists: DGIdb lists: DANPOS2 lists: CorrDrugTumorMSI lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: Dictyostelium discoideum genome database lists: DIAMOND lists: DichroWeb lists: DETONATE lists: DicomTypeTranslator lists: DIME lists: DEXSeq lists: DisProt - Database of Protein Disorder lists: D-EE lists: DAMBE lists: DiffBind lists: DiProGB lists: DOGMA lists: DSK lists: ENIGMA lists: Descriptions of Plant Viruses lists: DOMINE: Database of Protein Interactions lists: Dissect lists: DrivAER lists: Enrichr lists: Variant Effect Predictor lists: EBCall lists: eDMR lists: EMAN lists: Entrez Gene lists: ensembldb lists: Ensembl lists: Epigenomics Workflow on Galaxy and Jupyter lists: Ensembl Genomes lists: epitopepredict lists: DISENTANGLER lists: EpiDISH R package lists: ECLIPSE lists: Experimental Design Assistant lists: EpiGRAPH lists: European Variation Archive (EVA) lists: eQtlBma lists: Eukaryote Genes lists: EXOMEPICKS lists: fineSTRUCTURE lists: Evex lists: Evolutionary Couplings Server lists: Examl lists: NHLBI Exome Sequencing Project (ESP) lists: FlowSOM lists: FireDB lists: FGENESH lists: ExpressYourself lists: fgsea lists: FINDbase Worldwide lists: FateID lists: FluoRender lists: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application lists: FlexProt: flexible protein alignment lists: FlyBase lists: FLOSS lists: Full-Length cDNA Database lists: FANTOM DB lists: FragGeneScan lists: FuncAssociate: The Gene Set Functionator lists: FastQC lists: Genome Database for Rosaceae lists: Fugu Genome Project lists: FunRich: Functional Enrichment analysis tool lists: GASSST lists: G-Mo.R-Se lists: GeneCodis lists: GASV lists: FusionHunter lists: Genome Annotation Generator lists: GeneSeeker lists: GenePattern Notebook lists: GeCo3 lists: Gene3D lists: GeMoMa lists: GATK lists: Genome Projector lists: Genomedata lists: Gene Expression Atlas lists: GeneProf lists: Genome Trax lists: GENERECON lists: Genometa lists: GEDIT lists: FunCluster lists: Gibbs Motif Sampler lists: GEMB lists: Genome Reviews lists: GensearchNGS lists: GEPAT lists: Genomic Annotation in Livestock for positional candidate LOci lists: Generic GO Term Finder lists: GermOnline lists: VBASE2 lists: GEO2R lists: GFINDer: Genome Function INtegrated Discoverer lists: Generic GO Term Mapper lists: Google lists: Gene Ontology lists: Genome Aggregation Database lists: Gmove lists: Git lists: GNUMAP lists: G protein receptor interaction feature finding instrument lists: Graph2GO lists: Gaggle lists: GoMapMan lists: Gramene lists: GTDB-Tk lists: GO2MSIG lists: GMcloser lists: Genovar lists: Human Gene Mutation Database lists: H-InvDB lists: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology lists: GRASS lists: HTR lists: International HapMap Project lists: HASTE-project lists: HARSH lists: HAPLOCLUSTERS lists: HSSP lists: Homologous Sequences in Ensembl Animal Genomes lists: Human Splicing Finder lists: HPEPDOCK Server lists: HS-TDT lists: HubMed lists: IBIS: Inferred Biomolecular Interactions Server lists: hyfi: software suite for binding site search lists: HiCUP lists: Human Gene Connectome Server lists: Identifiers.org lists: HUGE - Human Unidentified Gene-Encoded large proteins lists: Hybrid-denovo lists: HINT lists: HUDSEN lists: IntEnz- Integrated relational Enzyme database lists: IMG System lists: HCLUST lists: iDASH lists: HiPipe lists: IMGT/StatClonotype lists: I-TASSER lists: IRESite lists: IMEx - The International Molecular Exchange Consortium lists: IMGT/HLA lists: ImJoy lists: IMGT HighV-QUEST lists: IMGT - the international ImMunoGeneTics information system lists: IsoEM lists: IPD - Immuno Polymorphism Database lists: iPiG lists: IPI lists: Isaac lists: Integr8 : Access to complete genomes and proteomes lists: inGAP lists: ISFinder lists: jmzML lists: Interolog/Regulog Database lists: IsoLasso lists: LAST lists: LOCUSMAP lists: J-Express lists: IsaCGH lists: IMG lists: lncRNAdb lists: InterProScan lists: KGGSeq lists: LDSELECT lists: Magic lists: JGI Genome Portal lists: lme4 lists: MAP lists: OntoQuest lists: Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains lists: MACiE lists: LitMiner lists: long-read-tools lists: LOCATE: subcellular localization database lists: LTR_FINDER_parallel lists: Maq lists: MaizeGDB lists: Mammalian Gene Collection lists: Machado lists: LRPath lists: MentaLiST lists: MatrixDB lists: MARRVEL lists: MEBS: Multigenomic Entropy-Based Score lists: Libra lists: LS-SNP/PDB lists: mapDamage lists: Maqview lists: Mascot lists: MAKER lists: MapSplice lists: MetAMOS lists: MethylExtract lists: MBGD - Microbial Genome Database lists: MB-GAN lists: MetaCyc lists: MeQA lists: MEGAHIT lists: Metabolomics Workbench lists: miRBase lists: Metastats lists: MBCluster.Seq lists: metaXplor lists: lsa_slurm lists: MeRIP-PF lists: MendelIHT.jl lists: proMODMatcher lists: mirTools lists: MetaCyto lists: MMAPPR lists: MICSA lists: MIRIAM Resources lists: MaSuRCA lists: UEA sRNA Workbench lists: MetaVelvet lists: miROrtho: the catalogue of animal microRNA genes lists: MERMAID lists: Mspire-Simulator lists: MULTIMAP lists: ML Repo lists: MIP Scaffolder lists: SCIPION lists: MPscan lists: MISA lists: MobiDB lists: MutPred lists: MizBee lists: MRFSEQ lists: MultiLoc lists: MP3 tool lists: Multi-omics Visualization Platform lists: NCBI Probe lists: NeLS lists: MoDIL lists: MPDA lists: Noncoding RNA database lists: Myriads lists: MUMmer lists: Multiple Myeloma survival predictor lists: mrCaNaVaR lists: MULTIDISEQ lists: mzMatch lists: Mouse Phenome Database (MPD) lists: NCBI lists: Ngs backbone lists: NetMHCpan Server lists: miRpathDB lists: NEMBASE lists: Nucleic Acid Database lists: NCBI Genome Workbench lists: NeuroMatic lists: Ngmlr lists: nsSNPAnalyzer lists: Nephele lists: Online Resource for Community Annotation of Eukaryotes lists: Omics Data Paper Generator lists: Necklace lists: NEST Simulator lists: Genotyping lists: NucleoFinder lists: NGSView lists: Open Trials lists: ngLOC lists: NetNGlyc lists: nmrML lists: NURD lists: ObjTables lists: Pathway Tools lists: NeSSM lists: NanoGalaxy lists: PartiGeneDB lists: NOrMAL lists: Open Babel lists: OsiriX Medical Imaging Software lists: PDB Finder lists: Opera lists: Pathbase lists: PEDIGREEQUERY lists: PAZAR lists: PDBe - Protein Data Bank in Europe lists: PanoramaWeb lists: Oncodrive-fm lists: parSMURF lists: Orientations of Proteins in Membranes database lists: PEDHUNTER lists: PeakAnalyzer lists: Illuminating the Druggable Genome lists: Phenotypes and eXposures Toolkit lists: PeakSeq lists: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers lists: PicTar lists: Pash 3.0 lists: Pedigree-Draw lists: OLego lists: Parliament2 lists: Phylogeny.fr lists: PEDPEEL lists: Plant Co-expression Annotation Resource lists: Peakzilla lists: Pfam lists: PhaseME lists: PHI-base lists: Eddy Lab Software lists: PhyML lists: Protein Information Resource lists: PRADA lists: PM4NGS lists: PennSeq lists: Philius lists: PeptideAtlas lists: PHYLIP lists: PhenoMan lists: Proteomics Identifications (PRIDE) lists: pNovo+ lists: ProfCom - Profiling of complex functionality lists: PIRSF lists: PubCrawler lists: PhyloPat lists: PEMA lists: Polygenic Pathways lists: pFind Studio: pLink lists: ProteomeXchange lists: PLANTTFDB lists: PyRosetta lists: Phospho.ELM lists: PRICE lists: PolymiRTS lists: PLINK/SEQ lists: PrimerBank lists: Pyntacle lists: PubChem lists: ProSight Lite lists: PubGene lists: PRED-TMBB lists: Preseq lists: ProtChemSI lists: R Project for Statistical Computing lists: RaptorX lists: QSRA lists: Protein Prospector lists: PrimerSeq lists: R/QTLBIM lists: Reactome lists: PyBEL lists: PS-Plant Framework lists: RepeatModeler lists: QuickGO lists: QmRLFS-finder lists: RefSeq lists: The Human Protein Atlas lists: QGene lists: PolyPhred lists: Rampart lists: ResponseNet lists: QUMA lists: QMSIM lists: RAREMETAL lists: Relate lists: ReactomePA lists: RESID lists: RADAR-base lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: R-SAP lists: Research-tested Intervention Programs (RTIPs) lists: RNA FRABASE - RNA FRAgments search engine and dataBASE lists: Reptile lists: Rdisop lists: RNA-SeQC lists: RNA Virus Database lists: RESCUE-ESE lists: REDItools lists: RegulonDB lists: SeqExpress lists: Scansite lists: RiboTaper lists: SALT lists: riborex lists: REDfly Regulatory Element Database for Drosophilia lists: rna-stability lists: RNAplex lists: rSNP Guide lists: SVA lists: RightField lists: runBioSimulations lists: SAMMate lists: SeqtrimNEXT lists: rSeq lists: SeqEM lists: ROMPREV lists: SeqSaw lists: SHARCGS lists: SAFA Footprinting Software lists: SHELX lists: sapFinder lists: QuPath lists: SIBLINK lists: Seqtk lists: SEEK lists: SMRT View lists: SKAT lists: SimRare lists: SeQuiLa lists: SGA lists: SASQUANT lists: Sherman lists: SilkDB lists: FASTSLINK lists: SASGENE lists: SILVA lists: SGD lists: ShinyGO lists: SimSeq lists: SIDER lists: SMI Services lists: Sniffles lists: STEPS lists: SNP HITLINK lists: SOAPnuke lists: SGN lists: SIBMED lists: SIMULATE lists: rnaSPAdes lists: SpliceMap lists: SMART lists: SnoopCGH lists: SynTView lists: SIMPED lists: Supersplat lists: SnpSift lists: SISSRs lists: Sybil lists: Solas lists: SNPTEST lists: SISYPHUS lists: ASC lists: SOAPfusion lists: TAndem Splice Site DataBase lists: SoupX lists: StSNP lists: T-lex lists: SWEEP lists: SynergyFinder lists: topGO lists: TAPIR: target prediction for plant microRNAs lists: TDT-PC lists: TDR Targets Database lists: SpoTyping lists: ShortFuse lists: SWISS-2DPAGE lists: Spot lists: TAGS lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs lists: SUMSTAT lists: TMAJ lists: TASSEL lists: TreeDyn lists: TropGENE DB lists: TB PORTALS lists: SwissTree lists: tradeSeq lists: FLUX CAPACITOR lists: UNAFold lists: Transporter Classification Database lists: ApiDB ToxoDB lists: Trowel lists: TopFIND lists: TRAL lists: Trim Galore lists: Biological General Repository for Interaction Datasets (BioGRID) lists: IQ-TREE lists: VirusSeq lists: Tool recommender system in Galaxy lists: V-Phaser 2 lists: SPIKE lists: Trans-ABySS lists: TRiCoLOR lists: TomoMiner lists: variancePartition lists: TRACESPipe lists: UTRdb/UTRsite lists: UniParc lists: TWOLOC lists: USeq lists: Zebrafish Information Network (ZFIN) lists: XPN lists: TransmiR lists: Webproanalyst lists: UTGB Toolkit lists: VAAST lists: VirusHunter lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: zUMIs lists: VaDiR lists: WSsas - Web Service for the SAS tool lists: VFDB - Virulence Factors of Bacterial Pathogens lists: Gene Index Project lists: Vector Alignment Search Tool lists: Vmatch lists: WEIGHTED FDR lists: Xenbase lists: xia2 pipeline lists: YASARA lists: Visualization and Analysis of Networks containing Experimental Data (VANTED) lists: VisSR lists: dbEST lists: DESeq2 lists: DNA DataBank of Japan (DDBJ) lists: FASTX-Toolkit lists: Trimmomatic lists: VIPERdb lists: PhenStat lists: ABySS lists: Integrative Genomics Viewer lists: Human Disease Ontology lists: LINKAGE lists: ConSurf Database lists: Protein Information Resource lists: PredictNLS lists: tRNAscan-SE lists: VeryFastTree lists: RSEM lists: Emboss Water lists: MEtabolomes, TRaits, and INteractions-Knowledge Graph is listed by: Debian is listed by: ELIXIR Tools and Data Services Registry is affiliated with: ELIXIR Tools and Data Services Registry is related to: ms-utils.org is related to: SUP	European Union Horizon 2020 ELIXIR-EXCELERATE grant 676559; Danish Ministry of Higher Education and Science	DOI:10.1186/s13059-019-1772-6 PMID:26538599	Free, Freely available	biotools:bio.tools, r3d100013668	https://github.com/bio-tools/biotoolsRegistry/, https://bio.tools/bio.tools, https://doi.org/10.17616/R31NJN1G	http://bio.tools	SCR_014695		2026-07-28 09:43:31	24
Debian Resource Report Resource Website 50+ mentions	Debian (RRID:SCR_006638)	Debian	data or information resource, database, source code, software resource, software repository	Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.	operating system, software package, FASEB list	lists: GUARDD lists: FACS lists: SNAVI lists: Fusion Analyser lists: GEOquery lists: MIMOSA lists: RNAcontext lists: AffyRNADegradation lists: Patchwork lists: GraBCas lists: GENIE3 lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: Megraft lists: PeptideProphet lists: VARiD lists: Flicker lists: ARACHNE lists: Quant lists: riboPicker lists: cn.FARMS lists: ProteinProphet lists: dbSTS lists: flowPeaks lists: SODOCK lists: PEPPER lists: POPBAM lists: Micro-Analyzer lists: MuTect lists: Mfuzz lists: PGS lists: TAPyR lists: ContEst lists: FPSAC lists: FlipFlop lists: SRMA lists: Pindel lists: PhenoFam lists: DSRC lists: SOAP lists: TriageTools lists: StringTie lists: SplitSeek lists: BLASR lists: Bowtie lists: Barrnap lists: MUSCLE lists: GimmeMotifs lists: massiR lists: CUDA-EC lists: Illuminator lists: SplicePlot lists: SLOPE lists: PARalyzer lists: VAAL lists: BreakSeq lists: ProGlycProt lists: OmicsOffice for NGS SeqSolve lists: TileQC lists: NGSUtils lists: QUAST lists: GenomicTools lists: piCALL lists: SNPchip lists: TALLYMER lists: SABER lists: wateRmelon lists: QualiMap lists: BFCounter lists: ADMIXTURE lists: OLIN lists: DEXUS lists: limmaGUI lists: KAnalyze lists: oneChannelGUI lists: BeadDataPackR lists: affylmGUI lists: SAMBLASTER lists: PyLOH lists: fRMA lists: CYCLE lists: FARMS lists: MACAT lists: GlyProt lists: YinOYang lists: Sequedex lists: DictyOGlyc lists: ToppCluster lists: Biocatalogue - The Life Science Web Services Registry lists: ProbRNA lists: HAPLOPAINTER lists: Chilibot: Gene and Protein relationships from MEDLINE lists: GERMLINE lists: FACTA+. lists: CisGenome lists: asSeq lists: unifiedWMWqPCR lists: HOMOZYGOSITYMAPPER lists: Prediction of Amyloid Structure Aggregation lists: InterMine lists: TANGO lists: CQN lists: MEME Suite - Motif-based sequence analysis tools lists: pRESTO lists: S-MART lists: PhosphoSitePlus: Protein Modification Site lists: myExperiment lists: DINDEL lists: Skylign lists: PEDIGRAPH lists: ADaCGH2 lists: CCAT lists: AnimalTFDB lists: TEMP lists: CanSNPer lists: Candida Genome Database lists: SamSPECTRAL lists: InteroPorc lists: MetaBase lists: Pecan lists: cisRED: cis-regulatory element lists: AffyPipe lists: SHORTY lists: BISC lists: Pathway Commons lists: Cake lists: SNVer lists: WebGeSTer DB lists: FlyFactorSurvey lists: ASPGD lists: TcoF lists: cpnDB: A Chaperonin Database lists: ZOOM lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: BEETL-fastq lists: NGSrich lists: ShotGun lists: Iterative Signature Algorithm lists: SBARS lists: SNPAAMapper lists: Autophagy Database lists: RUbioSeq lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: EchoBASE lists: QualitySNPng lists: Pathview lists: pymzML lists: RopeBWT2 lists: ExomeDepth lists: NetPathMiner lists: leeHom lists: PurBayes lists: libCSAM lists: SuperPred: Drug classification and target prediction lists: HGNC lists: Coding Potential Calculator lists: T3DB lists: CPTRA lists: BioNumbers lists: GATE lists: ProRata lists: GreenPhylDB lists: BREAKDANCER lists: GeneFisher lists: tweeDEseq lists: HYDEN lists: Eukaryotic Linear Motif lists: Primer3Plus lists: MethylAid lists: Triplex lists: Distant Regulatory Elements lists: hot scan lists: MFEprimer lists: Proteome Analyst Specialized Subcellular Localization Server lists: mrsFAST lists: BioJS lists: FastSNP lists: Gene Set Enrichment Analysis lists: Pipeliner lists: ms lims lists: GenePattern lists: rBiopaxParser lists: QDNAseq lists: MutDB lists: Piano lists: NovelSeq lists: MAGE-TAB lists: Database of Interacting Proteins (DIP) lists: Weighted Gene Co-expression Network Analysis lists: Blood Group Antigen Gene Mutation Database lists: drFAST lists: pairheatmap lists: MiST - Microbial Signal Transduction database lists: AltAnalyze - Alternative Splicing Analysis Tool lists: SplicingCompass lists: deFuse lists: Assembly Based ReAligner lists: ggbio lists: miR-PREFeR lists: ALDEx2 lists: HTqPCR lists: NanoStringNorm lists: T-profiler lists: Snakemake lists: jmzTab lists: MIPgen lists: Bpipe lists: PoPoolation lists: L-Measure lists: MultiPhen lists: PheWAS R Package lists: InsertionMapper lists: Quantitative Enrichment of Sequence Tags lists: INMEX lists: Segway - a way to segment the genome lists: SeWeR - SEquence analysis using WEb Resources lists: TagDust lists: BSRD lists: DER Finder lists: Stem Cell Discovery Engine lists: Kdetrees lists: Tree and reticulogram REConstruction lists: BioPig lists: NCBI BioSystems Database lists: Distributed String Mining Framework lists: NEWT lists: PILGRM lists: Selectome: a Database of Positive Selection lists: SVMerge lists: Parseq lists: SVseq lists: Small Molecule Pathway Database lists: miRNAKey lists: DELLY lists: Apo and Holo structures DataBase lists: BioSample Database at EBI lists: MetaPhyler lists: MG-RAST lists: SLIQ lists: SOPRA lists: Information Hyperlinked Over Proteins lists: AmphoraNet lists: SINA lists: SSPACE lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets lists: STING Report lists: G-BLASTN lists: RNA-eXpress lists: MethPipe lists: SoyBase lists: Strelka2 lists: RUM lists: SPOT - Biological prioritization after a SNP association study lists: VFS lists: PHAge Search Tool lists: MLTreeMap lists: SEECER lists: GeneTalk lists: ERANGE lists: rQuant lists: NCBO Annotator lists: ShoRAH lists: Yabi lists: ORMAN lists: FusionMap lists: CoPub lists: Scripture lists: SolexaQA lists: Kismeth lists: EMAGE Gene Expression Database lists: SAMStat lists: Knime4Bio lists: Bis-SNP lists: GobyWeb lists: Jellyfish lists: PRINSEQ lists: PASS lists: GSNAP lists: SOAPaligner/soap2 lists: MethylViewer lists: READSCAN lists: DistMap lists: MicrobesOnline lists: mrFAST lists: FLASH lists: TIGRFAMS lists: TMA Navigator lists: Bambino lists: TreQ lists: SeqMap lists: SeqTrace lists: TRANSFAC lists: GoFish lists: MethylomeDB lists: CLIPZ lists: SerbGO lists: ToppGene Suite lists: ngsTools lists: PePr lists: DMRforPairs lists: CharProtDB: Characterized Protein Database lists: Expression Profiler lists: SNPsandGO lists: GoSurfer lists: WEGO - Web Gene Ontology Annotation Plot lists: SOURCE lists: Stampy lists: DiseaseMeth lists: BLESS lists: GraphProt lists: GoPubMed lists: ccPDB - Compilation and Creation of datasets from PDB lists: Europe PubMed Central lists: Dr.VIS - Human Disease-Related Viral Integration Sites lists: DOMMINO - Database Of MacroMolecular INteractiOns lists: DBETH - Database for Bacterial ExoToxins for Humans lists: VirHostNet: Virus-Host Network lists: GWASdb lists: HFV Database lists: HotRegion - A Database of Cooperative Hotspots lists: eQuilibrator lists: FunTree lists: Cascade lists: 959 Nematode Genomes lists: ICEberg lists: IndelFR - Indel Flanking Region Database lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature lists: ProRepeat lists: NRG-CING lists: InterEvol database lists: MMMDB - Mouse Multiple tissue Metabolome DataBase lists: Newtomics lists: MIPModDB lists: DistiLD - Diseases and Traits in LD lists: Polbase lists: UMD-BRCA1/ BRCA2 databases lists: ScerTF lists: VIRsiRNAdb lists: ProPortal lists: OGEE - Online GEne Essentiality database lists: RecountDB lists: PRED-GPCR lists: RNA CoSSMos lists: PRED-SIGNAL lists: SNPedia lists: SpliceDisease lists: HMM-TM lists: deepSNV lists: OMPdb lists: PRED-LIPO lists: VICUNA lists: Predictive Networks lists: COEUS lists: GeneTrail lists: epigenomix lists: ADGO lists: SRAdb lists: QCGWAS lists: Flycircuit lists: MouseBook lists: Immune Epitope Database and Analysis Resource (IEDB) lists: SitEx lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: MSIsensor lists: TSSer lists: ATRHUNTER lists: Phytozome lists: Decombinator lists: ViralZone lists: COLT-Cancer lists: Gene Expression Database lists: BEDTools lists: waviCGH lists: Pseudomonas Genome Database lists: BIGpre lists: MyHits lists: CAPS Database lists: SpliceTrap lists: EagleView lists: IMGT/LIGM-DB lists: RIKEN integrated database of mammals lists: COHCAP lists: DARC - Database for Aligned Ribosomal Complexes lists: canSAR lists: GWAMA lists: AutismKB lists: zfishbook lists: PomBase lists: Myrna lists: PLEXdb - Plant Expression Database lists: RamiGO lists: PhenoM - Phenomics of yeast Mutants lists: IMGT/GENE-DB lists: HIstome: The Histone Infobase lists: SCOP: Structural Classification of Proteins lists: CuticleDB lists: agriGO lists: Expression Database in 4D lists: ESEfinder 3.0 lists: TriTrypDB lists: VIDA lists: Database of Arabidopsis Transcription Factors lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology lists: AgBase lists: Hyper Cell Line Database lists: Midbody, Centrosome and Kinetochore lists: Chromosome 7 Annotation Project lists: MfunGD - MIPS Mouse Functional Genome Database lists: Taipan lists: VISTA Browser lists: T1DBase lists: lobSTR lists: VISTA Enhancer Browser lists: MEROPS lists: Gene Array Analyzer lists: Network Analysis, Visualization and Graphing TORonto lists: Candidate Genes to Inherited Diseases lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) lists: eTBlast lists: hiPathDB - human integrated Pathway DB with facile visualization lists: MuSiC lists: miRNEST lists: QuasiRecomb lists: neXtProt lists: DNAtraffic lists: BeeBase lists: NetOGlyc lists: GenoTan lists: GMAP lists: LegumeIP lists: SeqBuster lists: elastix lists: iMir lists: WEBLOGO lists: MaCH-Admix lists: Pathema lists: SNPinfo Web Server lists: MOSCPHASER lists: NEBcutter lists: Atlas2 lists: FGDP lists: Velvet lists: HomSI lists: MicroSNiPer lists: MIRA lists: ALLPATHS-LG lists: CUPSAT lists: SVDetect lists: omiRas lists: CopySeq lists: MutSig lists: HapFABIA lists: DIANA-LncBase lists: MutationTaster lists: HMCan lists: Geneious lists: kmer-SVM lists: SICER lists: ZINBA lists: Pedimap lists: MAnorm lists: PlantTFcat lists: MethMarker lists: NPS lists: PeakRanger lists: SEAL lists: OligoArray lists: PSAR-Align lists: CEQer lists: CloudBurst lists: nucleR lists: RACE lists: Asterias lists: PatMaN lists: RobiNA lists: LitInspector lists: Btrim lists: ArrayAnalysis.org lists: CANGS lists: GeneStitch lists: ProDesign lists: JiffyNet lists: AlienTrimmer lists: GenoREAD lists: HSLPred lists: CancerResource lists: FABIA lists: PlnTFDB lists: easyRNASeq lists: OBI-Warp lists: PREDDIMER lists: ECHO lists: ICPL ESIQuant lists: PRIDE Converter 2 lists: SlideSort-BPR lists: COBRApy lists: MFPaQ lists: TopHat-Fusion lists: miRPlant lists: SNP ratio test lists: compomics-utilities lists: PLEK lists: multiplierz lists: Allim lists: ISDTool lists: NetCoffee lists: MToolBox lists: Scalpel lists: DNaseR lists: LocalAli lists: NAIL lists: iceLogo lists: GPU-Meta-Storms lists: AMS lists: rqubic lists: ANNOVAR lists: A5-miseq lists: PhosphoSiteAnalyzer lists: Cell motility lists: MethylCoder lists: CAZy- Carbohydrate Active Enzyme lists: CPFP lists: GENE-counter lists: PoolHap lists: LOCAS lists: CloudAligner lists: HeurAA lists: Mouse Genome Database lists: MitoBreak lists: PolyPhen: Polymorphism Phenotyping lists: GSA-SNP lists: featureCounts lists: Crossbow lists: CSAR lists: seqMINER lists: BEADS lists: IUPHAR/BPS Guide to Pharmacology lists: QuantiSNP lists: Cube-DB lists: Death Domain database lists: psRNATarget lists: DSAP lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase lists: GeneSigDB lists: MACS lists: NGSmethDB lists: GENSCAN lists: INCLUSive lists: MINAS - Metal Ions in Nucleic AcidS lists: Composition Profiler lists: NNcon lists: EGSEA lists: SCRATCH lists: Telescoper lists: Buccaneer lists: ProtTest lists: Morpheus lists: KAVIAR lists: DISEASES lists: SPEX2 lists: RAST Server lists: GeneWise lists: Crystallography and NMR System (CNS) lists: FATCAT lists: Membrane Protein Explorer lists: LTR_Finder lists: PALEOMIX lists: TISSUES lists: MetaMapR lists: primers4clades lists: MS-GF+ lists: PLAN2L lists: Off-Spotter lists: ProteomicsDB lists: CHiCAGO lists: SC3 lists: Bio-tradis lists: ApiDB CryptoDB lists: HISAT2 lists: PhyD3 lists: LoRDEC lists: Bamtools lists: ALTER lists: MultiQC lists: TFBS lists: EnrichmentMap lists: Poretools lists: Exonerate lists: 3D-footprint lists: Genesis lists: oligo lists: DISULFIND lists: Fastml lists: mentha lists: Oufti lists: eXpression2Kinases lists: IDEPI - IDentify EPItopes lists: SMAGEXP lists: ProCon - PROteomics CONversion lists: TRANSIT lists: DINIES lists: Splicing Express lists: FluxModeCalculator lists: Lifebit Deploit lists: ngsRelate lists: SARTools lists: OmicsNet lists: SPICE lists: Microscopy Image Browser lists: Thunder STORM lists: clusterProfiler lists: NetworkAnalyst lists: ANOCVA lists: Rsubread lists: Subread lists: ConsensusClusterPlus lists: CIBERSORT lists: FRETBursts lists: CCTOP lists: scran lists: ScaffMatch lists: Heatmapper lists: Goseq lists: PRSice lists: UMI-tools lists: Proovread lists: BinPacker lists: JAMM lists: CentroidFold lists: ComplexHeatmap lists: PatchDock lists: FastProject lists: ExPASy ABCD database lists: Gigwa lists: shinyGEO lists: GeSeq lists: EMBOSSMatcher lists: Geneshot lists: Mousebytes lists: trimAl lists: AmoebaDB lists: STRUCTURE lists: PASTEClassifier lists: NetPhos lists: HiC-Pro lists: SWISS-MODEL lists: Blood Exposome Database lists: HingeProt lists: ChiCMaxima lists: ProtParam Tool lists: GalaxyRefine lists: FlowCal lists: SpydrPick lists: R/qtl2 lists: Roary lists: SIGNOR lists: Protein Interactions Calculator lists: REDIportal lists: MaxAlign lists: Minimap2 lists: PrognoScan lists: GPS-SUMO lists: Signaling Pathways Project lists: ProSA-web lists: GalaxyWEB lists: iTOL lists: EpiModel lists: rVista lists: AlgPred lists: D-GENIES lists: Robetta lists: GOnet lists: E-CRISP lists: STAMP lists: Batch Web CD-Search Tool lists: aroma.light lists: Annotree lists: Database of Secondary Structure Assignments lists: Clustal Omega lists: DESeq lists: discoSnp lists: vcflib lists: Genome BioInformatics Research Lab - gff2ps lists: Primer3 lists: BioPerl lists: Rainbow lists: RNAhybrid lists: Clustal W2 lists: Apollo lists: IgBLAST lists: Ray lists: khmer lists: Stacks lists: Predictions for Entire Proteomes lists: DIALIGN lists: EBSeq lists: Minia lists: SAMtools/BCFtools lists: Artemis: Genome Browser and Annotation Tool lists: NCBI BLAST lists: biobambam lists: VICMpred lists: Staden Package lists: Bowtie 2 lists: RAxML lists: WHAM lists: VarScan lists: Bismark lists: ea-utils lists: HTSeq lists: Vienna RNA lists: Regulatory Sequence Analysis Tools lists: BitSeq lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: HilbertVis lists: BRIG lists: Unipro UGENE lists: GBrowse lists: Sickle lists: AmpliconNoise lists: FreeBayes lists: tRNAscan-SE lists: CD-HIT lists: SSAKE lists: MACH lists: Segemehl lists: BEAST lists: Pscan-ChIP lists: cutadapt lists: Oases lists: CGView lists: SOAPsnp lists: T-Coffee lists: Kalign lists: Circos lists: Trinity lists: Flexbar lists: SIFT lists: ProbCons lists: OpenMS lists: RSEM lists: Glimmer lists: GROMACS lists: CummeRbund lists: edgeR lists: DNAcopy lists: TopHat lists: SortMeRNA lists: LIMMA lists: AMOS lists: Cufflinks lists: Nanopolish lists: GMA lists: Prokka lists: phyloseq lists: SeqPrep lists: precrec lists: Atac lists: PAML lists: KisSplice lists: StoatyDive lists: IMGT-ONTOLOGY lists: KAT lists: SeaView lists: FastTree lists: Crux tandem mass spectrometry analysis software lists: rCASC lists: minet lists: becas lists: tximport lists: globaltest lists: CheckM lists: BLINK lists: mosdepth lists: bwtool lists: dcmqi lists: Pilon lists: ASHLAR lists: metagen lists: COPASI lists: BUSCO lists: bridge lists: TGS-GapCloser lists: NiftyPET lists: Blobtools lists: THESIAS lists: Fcirc lists: chimerascan lists: GLUE lists: SwiftOrtho lists: HaploReg lists: ScanITD lists: andi lists: metahdep lists: ImaGene lists: Jalview lists: MeroX lists: qrqc lists: BioNix lists: MiXCR lists: casper lists: libmgf lists: sleuth lists: imDEV lists: miRDB lists: yaqcaffy lists: NiftyFit lists: mlgt lists: SMARTdenovo lists: HH-suite lists: StatAlign lists: affy lists: shovill lists: Fiji lists: Racon lists: rbsurv lists: quantsmooth lists: tensorflow lists: seqbias lists: ngs.plot lists: bsseq lists: MGnify lists: dyebias lists: h5vc lists: ascat lists: Cuffdiff lists: mitopred lists: OrthoFinder lists: PIRATE lists: Bridger lists: Eoulsan lists: VEnCode lists: eTRIKS lists: fracridge lists: lumi lists: genomation lists: Hippocampome.org lists: SymPy lists: icy lists: GADMA lists: HaTSPiL lists: XL-mHG lists: ropls lists: scanpy lists: MethBase lists: sabre lists: plgem lists: MyGene.info lists: CRISPRcasIdentifier lists: biobakery lists: VETA lists: EpiEstim lists: HyPhy lists: ODAM lists: BISE lists: docker4seq lists: qcmetrics lists: Pavian lists: genehunter-imprinting lists: smashpp lists: NanoSim lists: SimVascular lists: BSA4Yeast lists: minfi lists: TDimpute lists: RepeatScout lists: neuroelectro lists: MRIcron lists: RepeatFiller lists: ShinyLearner lists: CRISPR-ERA lists: CRISPR-P lists: Warp lists: GEMINI lists: MAFFT lists: TransDecoder lists: Phenoscape lists: PhenoMeNal lists: les lists: Laniakea lists: CandiMeth lists: eisa lists: ProP Server lists: ggtree lists: scVelo lists: PathwayMatcher lists: charm lists: Telescope lists: skewer lists: multtest lists: Human Neocortical Neurosolver lists: beadarray lists: BioBERT lists: PlotTwist lists: GraphClust2 lists: METAREP lists: QIIME lists: halSynteny lists: scater lists: Galaxy scater lists: larvalign lists: iontree lists: VAPPER lists: GENCODE lists: Datanator lists: Bio2BEL lists: UALCAN lists: ffpe lists: MCScan lists: VisR lists: Metascape lists: GemSIM lists: EvidenceFinder lists: pepwheel lists: RDXplorer lists: bcbio-nextgen lists: OpenWorm lists: ActiveDriver lists: QuickNII lists: timecourse lists: Bionitio lists: ggplot2 lists: TCW lists: SPM lists: pvac lists: GeneMarkS-T lists: ascend lists: RatMine lists: CRISPRdirect lists: phantompeakqualtools lists: prank lists: refgenie lists: NanoPipe lists: vsn lists: PAFScaff lists: odMLtables lists: biospytial lists: NeuroChaT lists: clustergrammer lists: glycomedb lists: CLIP-Explorer lists: pheatmap lists: EnteroBase lists: GigaSOM.jl lists: bio.tools lists: SPP lists: lapmix lists: EHRtemporalVariability lists: HmtVar lists: SnpHub lists: Online Peri-Event Time Histogram for Open Ephys lists: NMRProcFlow lists: QGIS lists: Flye lists: kallisto lists: clipcrop lists: cn.mops lists: UniCarbKB lists: pickgene lists: PsyGeNET lists: seq-annot lists: PASA lists: ReadqPCR lists: breseq lists: e-Driver lists: sim4cc lists: PhylomeDB lists: fastqz lists: PerM lists: rnaQUAST lists: NCBI BioProject lists: PEMer lists: metabnorm lists: FusionCatcher lists: STAR lists: VCFtools lists: UniCarb-DB lists: NormqPCR lists: SnpEff lists: DecGPU lists: gprege lists: VirusMINT lists: nondetects lists: circlize lists: SAMTOOLS lists: Neuroscience Information Framework lists: Dali Server lists: IRanges lists: dbEST lists: Genomic Ranges lists: eProbalign lists: Cistrome lists: DIANA-mirPath lists: BpForms lists: GenomicFeatures lists: SOAPdenovo lists: BcForms lists: 4See lists: ABNER lists: A Classification of Mobile genetic Elements lists: Addgene lists: BadMedicine lists: ADMIXMAP lists: ADMIXTOOLS lists: ALCHEMY lists: AETIONOMY lists: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters lists: ALBERT lists: ALOHOMORA lists: Alternate splicing gallery lists: Allele Frequencies in Worldwide Populations lists: AmpliconTagger lists: Molecular Dynamics Workflow (BioKepler) lists: ape lists: Alta-Cyclic lists: Assisted Model Building with Energy Refinement (AMBER) lists: Aroma.affymetrix lists: ANDES lists: ASSOCIATIONVIEWER lists: ArrayMiner lists: ASPEX lists: The Alternatve Splicing Database lists: AutoAssemblyD lists: AutoDock Vina lists: BAIT lists: BamView lists: Avogadro lists: ArrayPipe lists: Athena lists: BLAT lists: BARS lists: BayesEpiModels lists: BatMeth lists: BeetleBase lists: BBSeq lists: naiveBayesCall lists: BarraCUDA lists: BCBtoolkit lists: BioConda lists: BAR lists: BiG-SLiCE lists: SVM based method for predicting beta hairpin structures in proteins lists: betaVAEImputation lists: BiNGO: A Biological Networks Gene Ontology tool lists: Bioinformatics Toolkit lists: BioCarta Pathways lists: Biopieces lists: Bio++ lists: BioPlex lists: BioSimulations lists: BRAIN lists: BOMP: beta-barrel Outer Membrane protein Predictor lists: biomaRt lists: bioSyntax lists: Bionimbus lists: BioSimulators lists: bioRxiv lists: Breakpointer lists: CiLiQuant lists: BSVF lists: BS Seeker lists: Bs-Seeker2 lists: BWA lists: CARD lists: Canu lists: Cell Image Library (CIL) lists: BRB-ArrayTools lists: CATALYST lists: CATH: Protein Structure Classification lists: CAT lists: CEM lists: CASPAR lists: CHEBI lists: ChimeraSlayer lists: CATdb: a Complete Arabidopsis Transcriptome database lists: ChemSpider lists: Chipster lists: CCREL lists: cisTEM lists: circlncRNAnet lists: Centrifuge Classifier lists: Cancer Genome Anatomy Project lists: ChIPMunk lists: Chromas lists: CiteFuse lists: CRCView lists: ChiRA lists: ClinVar lists: ClinTrajAn lists: clustLasso lists: CleanEx lists: Clinotator lists: CNVer lists: ComiR lists: CODEHOP lists: ClustVis lists: Comparative Metatranscriptomics Workflow lists: CMap lists: CorMut lists: CNV-seq lists: Coot lists: CITE-seq-Count lists: CoCo lists: CopyDetective lists: Chromosome Scale Assembler lists: cortex lists: ConDeTri lists: CRISPy-web lists: CONTRA lists: CovalentDock Cloud lists: CUDASW++ lists: COGEME Phytopathogenic Fungi and Oomycete EST Database lists: DANPOS2 lists: DOGMA lists: CorrDrugTumorMSI lists: DAMBE lists: D-EE lists: CoryneRegNet lists: ΔG prediction server lists: DIAMOND lists: CYANA lists: Datasets2Tools lists: DEXSeq lists: DichroWeb lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: DBTSS: Database of Transcriptional Start Sites lists: dbSNP lists: DiffBind lists: DETONATE lists: DiProGB lists: Descriptions of Plant Viruses lists: DIME lists: DicomTypeTranslator lists: CSDeconv lists: Dictyostelium discoideum genome database lists: DSK lists: DGIdb lists: DisProt - Database of Protein Disorder lists: DOMINE: Database of Protein Interactions lists: eDMR lists: ECLIPSE lists: Experimental Design Assistant lists: Dissect lists: Evolutionary Couplings Server lists: Enrichr lists: ensembldb lists: European Genome phenome Archive lists: EBCall lists: Ensembl Genomes lists: EMAN lists: ENIGMA lists: DISENTANGLER lists: Entrez Gene lists: Ensembl lists: eQtlBma lists: EpiGRAPH lists: EpiDISH R package lists: Examl lists: epitopepredict lists: DrivAER lists: Variant Effect Predictor lists: Epigenomics Workflow on Galaxy and Jupyter lists: Eukaryote Genes lists: Evex lists: FateID lists: EXOMEPICKS lists: European Variation Archive (EVA) lists: FANTOM DB lists: Genome Annotation Generator lists: FireDB lists: FGENESH lists: FluoRender lists: FLOSS lists: fineSTRUCTURE lists: FastQC lists: FINDbase Worldwide lists: ExpressYourself lists: fgsea lists: FuncAssociate: The Gene Set Functionator lists: NHLBI Exome Sequencing Project (ESP) lists: FlyBase lists: FlexProt: flexible protein alignment lists: GASV lists: Fugu Genome Project lists: Full-Length cDNA Database lists: FragGeneScan lists: FunRich: Functional Enrichment analysis tool lists: FlowSOM lists: GASSST lists: GeMoMa lists: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application lists: GEDIT lists: VBASE2 lists: Genome Database for Rosaceae lists: GenePattern Notebook lists: G-Mo.R-Se lists: FusionHunter lists: Genome Projector lists: GeneCodis lists: GEN3VA lists: GENERECON lists: GEMB lists: GeCo3 lists: Gene3D lists: Genomic Annotation in Livestock for positional candidate LOci lists: Gene Expression Atlas lists: GeneProf lists: Genome Trax lists: Genome Reviews lists: GATK lists: FunCluster lists: GFINDer: Genome Function INtegrated Discoverer lists: GermOnline lists: GeneSeeker lists: Gmove lists: Genometa lists: GensearchNGS lists: HARSH lists: Gibbs Motif Sampler lists: Generic GO Term Mapper lists: Genomedata lists: GMcloser lists: GEO2R lists: Gramene lists: Genome Aggregation Database lists: GoMapMan lists: GEPAT lists: Git lists: GNUMAP lists: Generic GO Term Finder lists: Graph2GO lists: Gene Ontology lists: Gaggle lists: GO2MSIG lists: GRASS lists: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology lists: Genovar lists: HASTE-project lists: H-InvDB lists: Homologous Sequences in Ensembl Animal Genomes lists: Google lists: IMGT/HLA lists: Human Gene Mutation Database lists: GTDB-Tk lists: G protein receptor interaction feature finding instrument lists: HubMed lists: HPEPDOCK Server lists: HUGE - Human Unidentified Gene-Encoded large proteins lists: HAPLOCLUSTERS lists: HiCUP lists: International HapMap Project lists: HiPipe lists: HTR lists: HINT lists: Hybrid-denovo lists: HS-TDT lists: Human Gene Connectome Server lists: HSSP lists: iDASH lists: hyfi: software suite for binding site search lists: HUDSEN lists: IMGT/StatClonotype lists: I-TASSER lists: ImJoy lists: IMEx - The International Molecular Exchange Consortium lists: IMG System lists: HCLUST lists: Human Splicing Finder lists: lme4 lists: Identifiers.org lists: IPD - Immuno Polymorphism Database lists: IntEnz- Integrated relational Enzyme database lists: IBIS: Inferred Biomolecular Interactions Server lists: IMGT - the international ImMunoGeneTics information system lists: Integr8 : Access to complete genomes and proteomes lists: IMGT HighV-QUEST lists: Isaac lists: Interolog/Regulog Database lists: InterProScan lists: IRESite lists: IPI lists: inGAP lists: ISFinder lists: KGGSeq lists: iPiG lists: IsoLasso lists: J-Express lists: JGI Genome Portal lists: IsaCGH lists: lncRNAdb lists: LDSELECT lists: IsoEM lists: Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains lists: IMG lists: LTR_FINDER_parallel lists: LAST lists: MBGD - Microbial Genome Database lists: jmzML lists: OntoQuest lists: LOCUSMAP lists: MaizeGDB lists: long-read-tools lists: LRPath lists: Magic lists: LS-SNP/PDB lists: LOCATE: subcellular localization database lists: Mammalian Gene Collection lists: Machado lists: MACiE lists: Maqview lists: LitMiner lists: MAKER lists: MEBS: Multigenomic Entropy-Based Score lists: MapSplice lists: Mascot lists: mapDamage lists: MEGAHIT lists: Metabolomics Workbench lists: Libra lists: ML Repo lists: MARRVEL lists: Maq lists: MentaLiST lists: MB-GAN lists: MetaCyc lists: MAP lists: MeQA lists: Metastats lists: MatrixDB lists: MetAMOS lists: MeRIP-PF lists: MendelIHT.jl lists: metaXplor lists: lsa_slurm lists: MetaCyto lists: UEA sRNA Workbench lists: MetaVelvet lists: MMAPPR lists: MBCluster.Seq lists: MIP Scaffolder lists: MERMAID lists: MobiDB lists: MPDA lists: MaSuRCA lists: MICSA lists: MIRIAM Resources lists: miROrtho: the catalogue of animal microRNA genes lists: NCBI lists: proMODMatcher lists: miRBase lists: MethylExtract lists: SCIPION lists: MPscan lists: mirTools lists: MISA lists: MP3 tool lists: Mspire-Simulator lists: Multi-omics Visualization Platform lists: mrCaNaVaR lists: MoDIL lists: MultiLoc lists: MULTIDISEQ lists: Noncoding RNA database lists: MRFSEQ lists: MizBee lists: Multiple Myeloma survival predictor lists: Mouse Phenome Database (MPD) lists: Nucleic Acid Database lists: Myriads lists: miRpathDB lists: MUMmer lists: mzMatch lists: NeLS lists: NEST Simulator lists: MutPred lists: NEMBASE lists: Open Babel lists: NetMHCpan Server lists: MULTIMAP lists: NCBI Genome Workbench lists: Nephele lists: NCBI Probe lists: Ngmlr lists: Necklace lists: NetNGlyc lists: NucleoFinder lists: NeuroMatic lists: Genotyping lists: NGSView lists: NOrMAL lists: Opera lists: NURD lists: ngLOC lists: NeSSM lists: NanoGalaxy lists: ObjTables lists: nmrML lists: nsSNPAnalyzer lists: OsiriX Medical Imaging Software lists: parSMURF lists: Open Trials lists: Ngs backbone lists: PartiGeneDB lists: Pfam lists: Oncodrive-fm lists: Online Resource for Community Annotation of Eukaryotes lists: PanoramaWeb lists: Omics Data Paper Generator lists: Pathway Tools lists: PDBe - Protein Data Bank in Europe lists: Pash 3.0 lists: Orientations of Proteins in Membranes database lists: Pathbase lists: PEDHUNTER lists: PAZAR lists: Peakzilla lists: PeakAnalyzer lists: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers lists: Pedigree-Draw lists: OLego lists: Parliament2 lists: PEDIGREEQUERY lists: PeakSeq lists: PEDPEEL lists: PhaseME lists: PHI-base lists: PHYLIP lists: PDB Finder lists: Phylogeny.fr lists: PRICE lists: PennSeq lists: Illuminating the Druggable Genome lists: Philius lists: Phenotypes and eXposures Toolkit lists: PhyloPat lists: PicTar lists: Eddy Lab Software lists: Protein Information Resource lists: PhyML lists: PhenoMan lists: PeptideAtlas lists: PIRSF lists: Polygenic Pathways lists: PLANTTFDB lists: pNovo+ lists: PLINK/SEQ lists: PEMA lists: pFind Studio: pLink lists: PM4NGS lists: PrimerBank lists: ProSight Lite lists: PolymiRTS lists: Phospho.ELM lists: Plant Co-expression Annotation Resource lists: Rampart lists: Protein Prospector lists: ProteomeXchange lists: PRED-TMBB lists: Proteomics Identifications (PRIDE) lists: PS-Plant Framework lists: ProtChemSI lists: PRADA lists: Pyntacle lists: PubCrawler lists: ProfCom - Profiling of complex functionality lists: PrimerSeq lists: PyBEL lists: PubChem lists: PubGene lists: R/QTLBIM lists: QGene lists: QMSIM lists: QmRLFS-finder lists: PolyPhred lists: QSRA lists: Preseq lists: ReactomePA lists: QuickGO lists: QUMA lists: RAREMETAL lists: REDItools lists: The Human Protein Atlas lists: rSNP Guide lists: PyRosetta lists: RefSeq lists: RaptorX lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: RegulonDB lists: RESID lists: R Project for Statistical Computing lists: Reactome lists: Rdisop lists: RepeatModeler lists: RESCUE-ESE lists: Relate lists: Reptile lists: R-SAP lists: riborex lists: RNA-SeQC lists: QuPath lists: RNA FRABASE - RNA FRAgments search engine and dataBASE lists: RADAR-base lists: RiboTaper lists: SAMMate lists: rna-stability lists: RightField lists: SASGENE lists: RNAplex lists: runBioSimulations lists: ResponseNet lists: SilkDB lists: Scansite lists: Research-tested Intervention Programs (RTIPs) lists: sapFinder lists: SeqtrimNEXT lists: RNA Virus Database lists: SALT lists: SEEK lists: Seqtk lists: REDfly Regulatory Element Database for Drosophilia lists: SAFA Footprinting Software lists: SeqExpress lists: ROMPREV lists: SeqSaw lists: SeqEM lists: SHELX lists: rSeq lists: SHARCGS lists: rnaSPAdes lists: SimSeq lists: SGA lists: Sherman lists: SeQuiLa lists: SGD lists: ShinyGO lists: SISYPHUS lists: SVA lists: ASC lists: SIMULATE lists: SILVA lists: SNP HITLINK lists: SIBLINK lists: SKAT lists: SimRare lists: SnoopCGH lists: SMRT View lists: SASQUANT lists: SIMPED lists: Sniffles lists: SIBMED lists: SMI Services lists: SOAPnuke lists: SGN lists: SIDER lists: SMART lists: ShortFuse lists: SWEEP lists: SnpSift lists: SOAPfusion lists: SNPTEST lists: SwissTree lists: TopFIND lists: Solas lists: SoupX lists: STEPS lists: FASTSLINK lists: SpliceMap lists: StSNP lists: Supersplat lists: Sybil lists: TAPIR: target prediction for plant microRNAs lists: SWISS-2DPAGE lists: SISSRs lists: T-lex lists: SUMSTAT lists: TAGS lists: Spot lists: TDR Targets Database lists: TDT-PC lists: SpoTyping lists: SynTView lists: SynergyFinder lists: TRAL lists: SPIKE lists: Transporter Classification Database lists: TransmiR lists: TASSEL lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs lists: FLUX CAPACITOR lists: TB PORTALS lists: TAndem Splice Site DataBase lists: VirusHunter lists: topGO lists: TMAJ lists: ApiDB ToxoDB lists: tradeSeq lists: TreeDyn lists: Trans-ABySS lists: IQ-TREE lists: Biological General Repository for Interaction Datasets (BioGRID) lists: Trowel lists: TomoMiner lists: UTRdb/UTRsite lists: TWOLOC lists: V-Phaser 2 lists: TropGENE DB lists: Trim Galore lists: TRACESPipe lists: Gene Index Project lists: Tool recommender system in Galaxy lists: WEIGHTED FDR lists: UTGB Toolkit lists: xia2 pipeline lists: USeq lists: TRiCoLOR lists: UniParc lists: VAAST lists: variancePartition lists: VirusSeq lists: Webproanalyst lists: XPN lists: WSsas - Web Service for the SAS tool lists: UNAFold lists: zUMIs lists: VaDiR lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: Vector Alignment Search Tool lists: Zebrafish Information Network (ZFIN) lists: YASARA lists: Vmatch lists: VFDB - Virulence Factors of Bacterial Pathogens lists: Xenbase lists: Visualization and Analysis of Networks containing Experimental Data (VANTED) lists: VisSR lists: AutoDock lists: dbEST lists: DESeq2 lists: DNA DataBank of Japan (DDBJ) lists: FASTX-Toolkit lists: SUP lists: Trimmomatic lists: VIPERdb lists: ABySS lists: AdapterRemoval lists: Alien-hunter lists: ALTree lists: Integrative Genomics Viewer lists: RDKit: Open-Source Cheminformatics Software lists: Acacia lists: AMAP lists: Anfo lists: Aragorn lists: Arden lists: Ariba lists: ART lists: Augustus lists: Axe lists: Baitfisher lists: BALLView lists: BEAGLE lists: BEDOPS lists: eXpress lists: BOXSHADE 3.21 lists: Cassiopee lists: Cdbfasta lists: Circlator lists: Clearcut lists: Clonalframe lists: ClonalOrigin lists: Computational Morphometry Toolkit lists: Concavity lists: CRAC lists: cwltool lists: Daligner lists: Datamash lists: DNACLUST lists: DWGSIM lists: Eigensoft lists: EMBOSS lists: ESTScan lists: EULER-SR lists: FASTLINK lists: FigTree lists: fitGCP lists: Fsm-lite lists: Gamgi lists: GASiC lists: Ghemical lists: GIIRA lists: Grinder lists: Gwyddion lists: Hmmer lists: HTQC lists: IDBA-UD lists: ImageJ lists: Infernal lists: PyMOL lists: GenABEL lists: Biopython lists: QuorUM lists: Prodigal lists: QuteMol lists: PRESTO: Genetic Association Analysis Software lists: Probalign lists: Computational Structural Biology Toolbox lists: LEfSe lists: Happy lists: jModelTest lists: KMC lists: LAMARC lists: libRoadRunner lists: LoFreq lists: MetaPhlAn lists: MicrobiomeUtilities lists: MINIMAC lists: MIPE lists: mothur lists: Mugsy lists: GNU Octave lists: Oncofuse lists: PBSIM lists: PerlPrimer lists: PHAST lists: Picard lists: PLINK lists: ADEGENET lists: phytools lists: PSCBS lists: R/QTL lists: SAM lists: vegan lists: RepeatMasker lists: Scythe lists: SEER lists: Seq-Gen lists: SMRT-Analysis lists: Scalable Nucleotide Alignment Program lists: SPAdes lists: TraceTuner lists: Transterm lists: TreeView lists: Viewmol lists: Vascular Modeling Toolkit lists: Aegean lists: amide lists: Anndata lists: ANTS - Advanced Normalization ToolS lists: ARB project lists: ArtificialFastqGenerator lists: Arvados lists: Bandage lists: Berkeley Advanced Reconstruction Toolbox lists: BBmap lists: Eagle lists: Bio-Formats lists: BioImage Suite lists: BioJava Project lists: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis lists: BRAKER 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Lipsia lists: LUMPY lists: Mash lists: Mesquite lists: MetaBAT lists: MOSAIK lists: MRtrix lists: Human Disease Ontology lists: NanoFilt lists: Object-Oriented Development Interface for NMR lists: OpenElectrophy lists: OpenMEEG lists: OpenWalnut lists: OptiType lists: PARASAIL lists: ParaView lists: PhyloPhlAn lists: Phyutility lists: Porechop lists: PSIPRED lists: PsychoPy lists: Pychopper lists: pydicom lists: PySurfer lists: MNE software lists: pbcore lists: pyxnat lists: QIIME2 lists: RAxML Next Generation lists: ShortRead lists: Phangorn lists: psych lists: VennDiagram lists: Recognition of Errors in Assemblies using Paired Reads lists: RELION lists: RStudio lists: Salmon lists: Scoary lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Short Read Sequence Typing for Bacterial Pathogens lists: Umap lists: VoxBo lists: WTDBG lists: XNAT - The Extensible Neuroimaging Archive Toolkit lists: ABACAS lists: AceDB lists: LINKAGE lists: Protein Information Resource lists: PredictNLS lists: tRNAscan-SE lists: RSEM lists: Aeskulap lists: alleleCount lists: assembly-stats lists: Atropos lists: Assemblytics lists: Augur lists: AxParafit lists: Aghermann lists: bambamc lists: AxPcoords lists: bamkit lists: BAli-Phy lists: Auspice lists: BBHash lists: BCALM 2 lists: Bibus lists: BioMAJ lists: BioCocoa lists: Biber lists: BioImageXD lists: caftools lists: BOLT-LMM lists: CamiTK lists: CLI for BioMAJ lists: CAMP lists: CAT and BAT lists: CHIME lists: CDK lists: ChromImpute lists: CiftiLib lists: conda-package-handling lists: CARD lists: CONTRAfold lists: CodonW lists: Change-O lists: C Thread Pool lists: Chemtool lists: covtobed lists: CTK lists: CTDopts lists: CTDConverter lists: Conquest DICOM lists: CTSim lists: Dicom3tools lists: Dendroscope3 lists: cyvcf2 lists: Deepbinner lists: EDFlib lists: EDFbrowser lists: dicompyler lists: EMMAX lists: DEXTRACTOR lists: DNApi lists: Epigrass lists: ELPH lists: ExaBayes lists: EMPeror lists: FreeImage lists: Fast5 Library lists: Entangle lists: FFP lists: GenomeTester4 lists: Filtlong lists: EMBOSS explorer lists: GfaPy lists: GATB lists: GCLib lists: EpiFire lists: HTSJDK lists: GDCM lists: GNUmed lists: GraphMap2 lists: foreign lists: Ginkgo CADx lists: GramAlign lists: IDeFIX lists: ImageTooth lists: Htscodecs lists: IGoR lists: iVar lists: InsPecT lists: Intake lists: IgDiscover lists: JAligner lists: ISMRMRD lists: JabRef lists: Lambda lists: Kaptive lists: KBibTeX lists: InSilicoSeq lists: kineticsTools lists: AcePerl lists: KmerResistance lists: Bio-EUtilities lists: Insight Toolkit lists: Kleborate lists: KMA lists: kempbasu lists: Bio-ASN1-EntrezGene lists: IVA lists: Bio-Coordinate lists: Bio-Graphics lists: AI-FANN lists: Bio-Chado-Schema lists: BioD lists: Bio-Tools-Run-Alignment-Clustalw lists: Bio-PrimerDesigner lists: Bioparser lists: Edlib lists: Bio-SamTools lists: libdisorder lists: libncl lists: Bio-Tools-Run-Alignment-TCoffee lists: Chado lists: Bio-Tools-Phylo-PAML lists: libGDF lists: JLODA lists: libdivsufsort lists: libminc lists: Bio-SCF lists: Sort-Key-Top lists: Java NeXML libraries and tools lists: libmaus2 lists: libqes lists: MIA lists: libics lists: FAST Analysis of Sequences Toolbox lists: Libchipcard lists: TaxonomyTree lists: Core Wrapper lists: Lighter lists: SSW Library lists: libqc++ lists: SeqLib lists: tabixpp lists: libStatGen lists: ThreadPool lists: Lucy lists: MafFilter lists: Metastudent lists: Libxdf lists: limereg lists: Mapsembler2 lists: MAXFLOW lists: metaBIT lists: MacSyFinder lists: VIGRA lists: MCL lists: MHAP lists: MindTheGap lists: Logol lists: medicalterms lists: mmtf-python lists: Miniasm lists: Tab2MAGE lists: MView lists: LTRsift lists: Molekel lists: mirtop lists: Maude lists: MicrobeGPS lists: mPSQed lists: mPTP lists: SMILE lists: Entrez Direct lists: NW-align lists: NanoSV lists: Mustang lists: Nanocall lists: Ngila lists: MRtrix3 lists: NORSp lists: Murasaki lists: Nextflow lists: NCBI accession download script lists: omegaMap lists: NJplot lists: NanoLyse lists: OpenCFU lists: NORSnet lists: OBITools lists: NeoBio lists: OptimiR lists: PartitionFinder lists: OpenSurgSim lists: NanoPlot lists: NextSV lists: OpenEMR lists: Orthanc lists: PAIPline lists: Odil lists: PHYLOViZ lists: PlasmidSeeker lists: PDB2PQR lists: OpenIGTLink lists: Parsnp lists: parallel-fastq-dump lists: ParsInsert lists: PiGx-RNAseq lists: PfTools lists: PlasmidID lists: Phyx lists: pipasic lists: pngquant lists: pbcopper lists: Patristic lists: PLIP lists: Placnet lists: PhySamp lists: pufferfish lists: PRINSEQ lists: PLAST lists: PCMA lists: picopore lists: POA lists: PROFisis lists: ProDA lists: PRANK lists: Cooler lists: pyepl lists: pssh2 lists: Plastimatch lists: pynast lists: psignifit lists: python-airr lists: Populations lists: pyFAI lists: python-biom-format lists: pyranges lists: purple lists: PyCogent lists: qtlreaper lists: qcumber lists: python-bx lists: pyomo lists: pycoqc lists: Proteinortho lists: DendroPy lists: qtltools lists: pyscanfcs lists: rambo-k lists: qcat lists: rasmol lists: rampler lists: raccoon lists: ragout lists: rapmap lists: quicktree lists: Raster3D lists: AnnotationHub lists: Rate4Site lists: altcdfenvs lists: annotate lists: biomformat lists: Biobase lists: affyio lists: bridgedbr lists: BiocGenerics lists: biovizBase lists: genefilter lists: CNEr lists: bsgenome lists: geneplotter lists: ctc lists: genomicalignments lists: go.db lists: genomeinfodb lists: hypergraph lists: gviz lists: groHMM lists: mergeomics lists: impute lists: makecdfenv lists: multiassayexperiment lists: qusage lists: mutationalpatterns lists: metagenomeseq lists: preprocesscore lists: pwmenrich lists: rbgl lists: htsfilter lists: nanostringqcpro lists: rgsepd lists: rcpi lists: pcaMethods lists: adephylo lists: rsamtools lists: savr lists: tfbstools lists: xvector lists: ade4 lists: biwt lists: beeswarm lists: cmprsk lists: alakazam lists: bio3d lists: Epi lists: BoolNet lists: DT lists: DoseFinding lists: itertools lists: fitdistrplus lists: fitbitscraper lists: dynamicTreeCut lists: epibasix lists: distory lists: forecast lists: incidence lists: hms lists: nmf lists: mediana lists: genetics lists: lexrankr lists: psychometric lists: optimalcutpoints lists: proc lists: pcapp lists: parmigene lists: rann lists: phylobase lists: psyphy lists: psychotree lists: rnexml lists: rook lists: rpact lists: tigger lists: robustrankaggreg lists: qqman lists: rwave lists: shazam lists: rsvd lists: rncl lists: rotl lists: rniftilib lists: sjplot lists: wavethresh lists: stringi lists: snowfall lists: waveslim lists: surveillance lists: tsne lists: webgestaltr lists: resfinder lists: readucks lists: recan lists: roadtrips lists: readseq lists: roguenarok lists: rtax lists: rgfa lists: ruby-bio lists: runcircos-gui lists: sailfish lists: samclip lists: saint lists: sambamba lists: seqmagick lists: sbmltoolbox lists: seq-seq-pan lists: seqsero lists: seqwish lists: shapeit4 lists: sepp lists: crb-blast lists: sigma-align lists: sibsim4 lists: signalalign lists: sibelia lists: shiny-server lists: sistr lists: skesa lists: sigviewer lists: snpomatic lists: spaced lists: sitplus lists: sofa-apps lists: sra-toolkit lists: strap-base lists: sparta lists: swarm lists: sourmash lists: surankco lists: streamlit lists: tab2mage lists: sumaclust lists: sweed lists: tacg lists: zAlign lists: tiddit lists: Workrave lists: sprai lists: VolPack lists: XMedCon lists: Yanosim lists: Yanagiba lists: libswiss-perl lists: yaha lists: VisIt lists: VelvetOptimiser lists: variation graph lists: vcfanno lists: VarMatch lists: VirulenceFinder lists: CCS lists: VADR lists: VARNA lists: VMD lists: FISH lists: trace2dbEST lists: TREE-PUZZLE lists: umis lists: Trinculo lists: toil lists: TRANSIT lists: toppred lists: Unicycler lists: TM-align lists: Tn-seq explorer lists: Tombo lists: TopHat-Recondition is related to: FreeContact is parent organization of: neurodebian			Free, Freely available	nlx_151598			SCR_006638	Debian - The universal operating system, Debian GNU/Linux	2026-07-28 09:41:39	50

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