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Resource Name Sort Ascending Sort Descending	Proper Citation Sort Ascending Sort Descending	Abbreviations Sort Ascending Sort Descending	Resource Type Sort Ascending Sort Descending	Description	Keywords Sort Ascending Sort Descending	Resource Relationships Sort Ascending Sort Descending	Funding Sort Ascending Sort Descending	Defining Citation Sort Ascending Sort Descending	Availability	Alternate IDs	Alternate URLs	Old URLs	Resource ID	Synonyms Sort Ascending Sort Descending	Record Last Update Sort Ascending Sort Descending	Mentions Count Sort Ascending Sort Descending
ChIP-Atlas Resource Report Resource Website 100+ mentions	ChIP-Atlas (RRID:SCR_015511)		data or information resource, web application, database, software resource	Database for visualizing and making use of public ChIP-seq data. ChIP-Atlas covers almost all public ChIP-seq experiments and data submitted to the SRA (Sequence Read Archives) in NCBI, DDBJ, or ENA.	chip-seq, sequence read archive, sequencing, FASEB list	is listed by: OMICtools has parent organization: Kyushu University; Fukuoka; Japan has parent organization: NBDC - National Bioscience Database Center			Freely Available				SCR_015511		2026-08-10 09:35:31	477
OMICtools Resource Report Resource Website 10+ mentions	OMICtools (RRID:SCR_002250)	OMICtools	data or information resource, database, catalog	THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.	metadatabase, manually, curated, tool, genomic, transcriptomic, proteomic, metabolomic, data	lists: ncdfFlow lists: BSmooth-align lists: 4Peaks lists: CSDeconv lists: Tablet lists: GenomicRanges lists: SNPSVM lists: ReadqPCR lists: SP-Designer lists: CorMut lists: ChIPmeta lists: FACS lists: metaSeq lists: Dissect lists: Fusion Analyser lists: FusionCatcher lists: GASV lists: GHOSTM lists: nFuse lists: PD5 lists: Patchwork lists: QuadGT lists: VariantAnnotation lists: ReQON lists: SnowsShoes-FTD lists: timecourse lists: SOAPfuse lists: SOAPfusion lists: pFind Studio: pLink lists: Spotfinder lists: AbMining ToolBox lists: SNAVI lists: MetAssign lists: JChemPaint lists: siRNArules lists: AutoPrime lists: RmiR.Hs.miRNA lists: MysiRNA-designer lists: TACOA lists: Treephyler lists: MedGen lists: D-Tailor lists: BioLemmatizer lists: AffyRNADegradation lists: Orphelia lists: ArrayExpress (R) lists: Parallel-META lists: CovalentDock Cloud lists: DOCK lists: exomeSuite lists: SPAdes lists: Sequence Read Format lists: FastQ Screen lists: GEOquery lists: Bovine Genome Database lists: GISTIC lists: DESeq lists: Postgwas lists: BLASTPLOT lists: miRanalyzer lists: Magnolya lists: GMATo lists: GemSIM lists: Grinder lists: Illuminate lists: RNAcontext lists: MIMOSA lists: F2DockClient lists: FlexX lists: Glide lists: GOLD lists: Molegro Virtual Docker lists: Sanjeevini lists: SODOCK lists: HEM lists: Surflex-Dock lists: Cascleave lists: MetaDE lists: Cell Death Proteomics Database lists: GPS-Calpain Cleavage Detector lists: GraBCas lists: c3net lists: Context Likelihood of Relatedness lists: GENIE3 lists: Inferelator lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: MRNet lists: UnSplicer lists: Duplicate reads removal lists: PEpiD lists: TAPIR: target prediction for plant microRNAs lists: iOMICS lists: Megraft lists: VARiD lists: Cistrome lists: PSGInfer lists: MochiView lists: RSEM lists: RNAmotifs lists: M(at)CBETH lists: MS-Spectre lists: Quant lists: RNASeqReadSimulator lists: iFad lists: GramCluster lists: GProX lists: PeptideProphet lists: CNTools lists: Lasergene's SeqMan Pro lists: ProteinProphet lists: OMSSAPercolator lists: Flicker lists: cn.FARMS lists: LIPAGE lists: DNASTAR: Lasergene Core Suite lists: Clonality lists: oneClickCGH lists: CGH Fusion lists: Screensaver lists: fqzcomp lists: ArrayPlex lists: MiRdup lists: MeQA lists: Methyl-Analyzer lists: Annotare lists: CpGassoc lists: Koadarray lists: RADtools lists: rtd lists: ABrowse lists: GPViz lists: cuteNMR lists: Jnomics lists: JMolDraw lists: CGAP-Align lists: ARACHNE lists: Kinannote lists: CLC Main Workbench lists: ParseCNV lists: TAPS lists: PyroHMMsnp lists: TransView lists: pvac lists: riboPicker lists: NucleoFinder lists: bzip2 lists: GENSENG lists: AS-Peak lists: is-rSNP lists: ILLUMINUS lists: QUALIFIER lists: FunctSNP lists: Micro-Analyzer lists: flowStats lists: flowPeaks lists: metaMA lists: rTANDEM lists: flowFlowJo lists: TargetCaller lists: PSCBS lists: iASeq lists: d2-tools lists: PEPPER lists: OLINgui lists: TNO-DECO lists: SigFuge lists: stsPlots lists: Sulfinator lists: Rdisop lists: pbcore lists: GeneExpressionSignature lists: sybil - Efficient Constrained Based Modelling in R lists: msbwt lists: MetaDrug lists: Reprever lists: POPBAM lists: SAMBLASTER lists: SpeedSeq lists: pyQPCR lists: RefFinder lists: PGS lists: miRprimer lists: iBMQ lists: NIMBL lists: TDARACNE lists: bamova lists: BAIT lists: ARNIE lists: fourSig lists: Mfuzz lists: MaryGold lists: TOPPAS lists: SPHINX lists: PhyloPythia lists: MATCHCLIP lists: mzMatch lists: Sequence Search and Alignment by Hashing Algorithm lists: ESPRIT lists: DySC lists: FPSAC lists: Scaffold builder lists: SNPiR lists: ACCUSA2 lists: MuTect lists: Pindel lists: rSeq lists: GERP lists: SiPhy lists: wANNOVAR lists: ViReMa lists: Smart Dictionary Lookup lists: VariantMaster lists: GeneWays lists: AdaptiveCrawler lists: NGS-Cleaner lists: flowQ lists: Database Enabled Code for Ideal Probe Hybridization Employing R lists: NGSmethPipe lists: Pyrocleaner lists: DecGPU lists: drFAST lists: MPscan lists: TAPyR lists: MutPred Splice lists: ContEst lists: Mini Analysis Guide for Microarrays lists: DDBJ Omics Archive lists: Chromas lists: OnEx - Ontology Evolution Explorer lists: BEBaC lists: FlipFlop lists: Phosphor Antibody Array Data Analysis lists: PhenoFam lists: forqs lists: GMcloser lists: GenomeWeb lists: Bycom lists: CorQ lists: NGS tools for the novice lists: Opera lists: SRMA lists: DeNovoGear lists: VarB lists: BAMseek lists: TriageTools lists: clipcrop lists: detecttd lists: FastUniq lists: GEUVADIS lists: TMAP lists: BISMA lists: FineSplice lists: RMAP lists: Sequencing Analysis Software lists: BLASR lists: GlycoWorkbench lists: jmzIdentML API lists: SciRoKo lists: HapCompass lists: JBrowse lists: DSRC lists: fastqz lists: GDC lists: GRS lists: PREFAB lists: BLASTP lists: Google Compute Engine lists: SplitSeek lists: ASC lists: NPEBseq lists: FUSIM lists: Geoffs Bio-Directories lists: Phred lists: MassGenomics lists: Illuminator lists: BAC lists: targetscan.Hs.eg.db lists: RmiR lists: MmPalateMiRNA lists: Starr lists: bsseq lists: Qvalue lists: ExomePeak lists: NextGenSeq(at)nature.com lists: AutoAssemblyD lists: CUDA-EC lists: rGADEM lists: qips lists: PICS lists: Jmosaics lists: SparseAssembler lists: BreakFusion lists: ParticleCall lists: DSGseq lists: R453Plus1Toolbox lists: SynView lists: ShortFuse lists: Cancer Gene Index lists: jmzML lists: CASVM lists: Birdseed lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: GimmeMotifs lists: skewer lists: flowWorkspace lists: massiR lists: Transposon Insertion Finder lists: Shimmer lists: GenVision lists: DiMO lists: MetaPhyl lists: WiggleTools lists: EMI lists: SplicePlot lists: CrossMap lists: GraphIBD lists: rbsurv lists: Skylign lists: HMMvar lists: tbvar lists: STRViper lists: Breakway lists: Genometa lists: CATCHprofiles lists: VAAL lists: SLOPE lists: BreakSeq lists: Anchored Assembly lists: Bionimbus lists: ChIPMunk lists: RDPipeline lists: PeakAnalyzer lists: SomaticCall lists: Baa.pl lists: VirusHunter lists: seq2HLA lists: MUMmerGPU lists: GeneMeta lists: GenoMiner lists: GenoViewer lists: sim4cc lists: GenomicTools lists: Omixon Target HLA Typing lists: Omixon Target Data Analysis lists: PARalyzer lists: QualiMap lists: Lab7 lists: mlgt lists: BSSim lists: Golden Helix GenomeBrowse lists: HiPipe lists: MADAM lists: Microarray Data Analysis System lists: Automated Microarray Pipeline lists: MergeMaid lists: OmicsOffice for NGS SeqSolve lists: categoryCompare lists: metahdep lists: Plantagora lists: QUAST lists: TileQC lists: VectorFriends lists: vcflib lists: PHACCS lists: Sequedex lists: Genome Trax lists: VCFtools lists: NGSUtils lists: ChIP-seq lists: Tally lists: mapDamage lists: freeIbis lists: piCALL lists: ERGO lists: TALLYMER lists: KMC lists: DSK lists: Mutation Surveyor lists: BFCounter lists: snpStats: SnpMatrix and XSnpMatrix classes and methods lists: CNVtools lists: CGEN lists: RCASPAR lists: iterativeBMAsurv lists: multtest lists: globaltest lists: SABER lists: Local Ancestry in adMixed Populations lists: GemTools lists: MinimumDistance lists: ipPCA lists: ADMIXTURE lists: frappe lists: Mutascope lists: metabnorm lists: VegaMC lists: VanillaICE lists: SNPchip lists: SMAP lists: quantsmooth lists: mBPCR lists: ITALICS lists: GenoSet lists: exomeCopy lists: CGHregions lists: CGHbase lists: BlindCall lists: beadarraySNP lists: SSCprofiler lists: CGH-Explorer lists: GLAD lists: SNP and Variation Suite SNP Analysis lists: SNP and Variation Suite CNV Analysis lists: ProbRNA lists: methylMnM lists: methyAnalysis lists: les lists: ARRmNormalization lists: ChIPsim lists: Sherman lists: yaqcaffy lists: wateRmelon lists: sRAP lists: spotSegmentation lists: SNM lists: SNAGEE lists: Simpleaffy lists: qcmetrics lists: OLIN lists: MANOR lists: limmaGUI lists: ffpe lists: dyebias lists: DEXUS lists: BeadDataPackR lists: aroma.light lists: ArrayTools lists: beadarray lists: arrayQuality lists: arrayMvout lists: affyQCReport lists: affyPLM lists: affylmGUI lists: AffyExpress lists: waveTiling lists: KAnalyze lists: gprege lists: oneChannelGUI lists: CYCLE lists: LMGene lists: factDesign lists: pickgene lists: betr lists: NGSrich lists: SCAN.UPC lists: arrayQualityMetrics lists: CALIB lists: DEDS lists: Harshlight lists: MiChip lists: OCplus lists: bridge lists: FARMS lists: fRMA lists: genArise lists: lapmix lists: maCorrPlot lists: maSigPro lists: MACAT lists: maigesPack lists: MDQC lists: metaArray lists: nnNorm lists: plgem lists: PVCA lists: RAMA lists: stepNorm lists: virtualArray lists: LPE lists: DDBJ Sequence Read Archive lists: WegoLoc lists: Mugsy lists: Mspire-Simulator lists: CytoSPADE lists: vsn lists: ACME lists: GenGIS lists: CoGAPS lists: NTAP lists: ToppCluster lists: PyLOH lists: Nebula lists: Sequencher lists: flowFP lists: ChIPseeqer lists: CisGenome lists: CGHcall lists: rMAT lists: TileMap lists: Clustal Omega lists: BLASTN lists: SeqScape Software lists: BACContigEditor lists: Human Gene Mutation Database lists: AnimalTFDB lists: asSeq lists: Cuffdiff lists: BLASTX lists: SLqPCR lists: rSeqDiff lists: AffinDB lists: Enriched Domain Detector lists: A Classification of Mobile genetic Elements lists: PELICAN lists: nondetects lists: rlsim lists: Chilibot: Gene and Protein relationships from MEDLINE lists: unifiedWMWqPCR lists: HAPLOPAINTER lists: HOMOZYGOSITYMAPPER lists: QuasiSeq lists: sSeq lists: GERMLINE lists: MCMC.qpcr lists: CNVrd2 lists: TaLasso lists: pairedBayes lists: RNASeqBias lists: plateCore lists: PLINK lists: MACH 1.0 lists: PennSeq lists: FACTA+. lists: Prediction of Amyloid Structure Aggregation lists: TANGO lists: DNACLUST lists: InterMine lists: MSClust lists: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets lists: RSVSim lists: TCC lists: SAMstrt lists: pRESTO lists: MEME Suite - Motif-based sequence analysis tools lists: PoissonSeq lists: CQN lists: GLiMMPS lists: TEMP lists: BEAGLE lists: SPP lists: BIRDSUITE lists: NASTIseq lists: BREAKDANCER lists: CAROL lists: COMPASS lists: CASAVA lists: flowClust lists: HSA lists: SPADE lists: AStalavista lists: Visual Molecular Dynamics lists: EXTREME lists: CYRILLIC lists: DINDEL lists: ASprofile lists: OrderedList lists: GenABEL lists: CCAT lists: Alt Event Finder lists: BroadPeak lists: SamSPECTRAL lists: THetA lists: TCW lists: GATK lists: Degust lists: flowUtils lists: DAVID lists: RchyOptimyx lists: StatAlign lists: Arabidopsis thaliana Protein Interactome Database lists: FGED lists: ExpressionPlot lists: S-MART lists: Pecan lists: SeqMonk lists: Ray lists: tbrowse lists: Bacteriome.org lists: Apollo lists: RAVEN lists: PEDIGRAPH lists: BAliBASE lists: TEQC lists: rSNPs MAPPER lists: rSNPBase lists: SNP Function Portal lists: flowType lists: SNPper lists: MADELINE lists: CanSNPer lists: ADaCGH2 lists: SGA lists: NormaCurve lists: GapMis lists: TRAMS lists: SNPMeta lists: SNPAAMapper lists: METAL lists: OLORIN lists: openADAM lists: SeqEM lists: SHARCGS lists: DMET-Analyzer lists: PEDHUNTER lists: AffyPipe lists: pSTIING lists: PTMcode lists: SHORTY lists: POLYMUTT lists: TissueNet - The Database of Human Tissue Protein-Protein Interactions lists: TRIP Database lists: SNVer lists: BISC lists: Primate Orthologous Exon Database lists: PurBayes lists: PyroHMMvar lists: flowViz lists: ChIPSeq Peak Finder lists: SpliceAid-F lists: Vennt lists: flowTrans lists: Spliceosome Database lists: cisRED: cis-regulatory element lists: ASPicDB lists: SAMTOOLS lists: HEXEvent lists: DBASS lists: FlyFactorSurvey lists: SNAP - SNP Annotation and Proxy Search lists: STIFDB lists: Cake lists: MPromDb lists: ProTISA lists: circlize lists: AmiGO lists: flowQB lists: Cinteny lists: RegPrecise lists: STRUCTURE lists: SVA lists: SYZYGY lists: TcoF lists: Matchprot lists: WebGeSTer DB lists: pfSNP lists: shinyTANDEM lists: CistromeMap lists: metaRNASeq lists: ZOOM lists: flowPlots lists: ImaGene lists: VAAST lists: ARACNE lists: FR-HIT lists: PROVEAN lists: flowPhyto lists: flowCore lists: flowMerge lists: RankAggreg lists: ConsensusPathDB lists: MAIA (Microarray Image Analysis) lists: CORUM lists: CoryneRegNet lists: miso-lims lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: cpnDB: A Chaperonin Database lists: flowMap lists: rmeta lists: flowMeans lists: CTCFBSDB lists: spliceR lists: flowMatch lists: flowFit lists: DEMI lists: Binding MOAD lists: DBD: Transcription factor prediction database lists: CodonCodes TraceViewer lists: RelocaTE lists: MAGE lists: flowCyBar lists: Iterative Signature Algorithm lists: Variant Reporter Software lists: RepARK lists: PolyPhred lists: dbSNP lists: BEETL-fastq lists: DWGSIM lists: Ensembl lists: DBTBS lists: MIAME lists: MAQC lists: HaploClique lists: DBTSS: Database of Transcriptional Start Sites lists: DNA DataBank of Japan (DDBJ) lists: ISO lists: SBARS lists: Clinical and Laboratory Standards Institute lists: JGI Genome Portal lists: Cancer Genomics Consortium lists: BEAT lists: DOMINO: Domain peptide interactions lists: R Tutorial - An R Introduction to Statistics lists: R Tutorial lists: DOMINE: Database of Protein Interactions lists: GenomeSmasher lists: DOSY Toolbox lists: MUMA lists: Database of Rice Transcription Factors lists: VennDiagram lists: Quick-R lists: EcoCyc lists: Tree of Life lists: flowBeads lists: EDAS - EST-Derived Alternative Splicing Database lists: eggNOG lists: NRDR lists: YLoc lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: EID: Exon-Intron Database lists: WoLF PSORT lists: Entrez Gene lists: Mason lists: QualitySNPng lists: EPDnew lists: realSFS lists: pymzML lists: RUbioSeq lists: PBSIM lists: PennCNV lists: pIRS lists: PeptideShaker lists: ShotGun lists: Gibbs Motif Sampler lists: Zebrafish Information Network (ZFIN) lists: Wessim lists: BioStar lists: MBASED lists: discoSnp lists: RVD lists: SEEK lists: MethylAid lists: ExomeDepth lists: libmgf lists: Autophagy Database lists: T3DB lists: RopeBWT2 lists: e-Driver lists: sapFinder lists: PharmGKB lists: CTF lists: SuperTarget lists: DrugBank lists: PANDAseq lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: leeHom lists: Reflect lists: Mapix lists: Rainbow lists: CASBAH lists: TelSeq lists: Pathview lists: GLProbs lists: rBiopaxParser lists: DSS lists: GATE lists: NetPathMiner lists: NMR metabolomics database of Linkoping lists: GenBank lists: HINT lists: libCSAM lists: RNA Abundance Database lists: GeneCards lists: BINOCh lists: AliView lists: TherMos lists: ANDES lists: PacmonSTR lists: RMassBank lists: FisHiCal lists: Mutation Annotation and Genomic Interpretation lists: Circleator lists: IMEx - The International Molecular Exchange Consortium lists: Batch Oligo Selection Script lists: iontree lists: MicroVigene lists: Greengenes lists: Basic4Cseq lists: rDock lists: hot scan lists: International HapMap Project lists: BiGGR lists: mzR lists: PAPi lists: pNovo+ lists: COV2HTML lists: CODEHOP lists: CNVassoc lists: PRO lists: Hollywood lists: StreamingTrim lists: pLabel lists: HomoloGene lists: aCGH.Spline lists: pBuild lists: Time-series RNA-seq Analysis Package lists: CGHnormaliter lists: Type-III-Secretion-System related database lists: SMRT-Analysis lists: CPTRA lists: mtDB - Human Mitochondrial Genome Database lists: AltAnalyze - Alternative Splicing Analysis Tool lists: Chimera lists: IMG System lists: Babelomics lists: MRFSEQ lists: ms lims lists: ChIPMonk lists: Gel2DE lists: UCSF Spot lists: ProRata lists: R-pbutils lists: MITOMAP - A human mitochondrial genome database lists: NOISeq lists: Dpos lists: Gene Weaver lists: pFind lists: Canadian College of Medical Geneticists lists: BRAIN lists: Isopat lists: R-pbh5 lists: pbh5tools lists: SMRT View lists: JASPAR lists: enviPat lists: bwtool lists: MoSDi lists: tweeDEseq lists: DIALIGN lists: PacBioToCA lists: DiNuP lists: Gutentag lists: Parametric Time Warping lists: SurvComp lists: SASqPCR lists: enviPick lists: GeneFisher lists: Triplex lists: MPprimer lists: MIPE lists: MFEprimer lists: DnaSP lists: FAS-DPD lists: SURPI lists: MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation lists: MachiBase lists: Primer3Plus lists: e-PCR lists: NeuroMab lists: In-Silico PCR lists: JETTA lists: MapViewer lists: Primer-BLAST lists: WormBase lists: eQtlBma lists: JuncBASE lists: MethDB lists: pairheatmap lists: MISO lists: HYDEN lists: mrsFAST lists: PredictNLS lists: mrCaNaVaR lists: NovelSeq lists: PlantLoc lists: Primer3 lists: FastSNP lists: Proteome Analyst Specialized Subcellular Localization Server lists: NYCE lists: GeneScissors lists: ngLOC lists: MultiLoc lists: GeneCruiser lists: MetaLocGramN lists: FastPCR lists: miRNAMap lists: HUPO Proteomics Standards Initiative lists: SaskPrimerFS lists: rDiff lists: Database of Interacting Proteins (DIP) lists: Solas lists: Pipeliner lists: iLoc-Animal lists: QDNAseq lists: ResponseNet lists: SynSysNet lists: XORRO lists: Stacks lists: SECISearch3 and Seblastian lists: SALT lists: HyperTree lists: Primer Designer lists: r3Cseq lists: Gene Set Enrichment Analysis lists: Piano lists: PHAST lists: NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects lists: NGSadmix lists: Gemi lists: Talking Glossary of Genetic Terms lists: PathGuide: the pathway resource list lists: SplicingCompass lists: RNAhybrid lists: LUMPY lists: Geospiza lists: SpliCQ lists: ORFprimer lists: JCVI Primer Designer lists: Assembly Based ReAligner lists: deFuse lists: Xenbase lists: PoPoolation2 lists: OmicCircos lists: Amplicon lists: PrimerSeq lists: Genedata Expressionist lists: biobambam lists: RCircos lists: ggbio lists: DAFGA lists: MIPgen lists: PicTar lists: BlockClust lists: PIRSF lists: miR-PREFeR lists: MouseNET lists: PlantProm DB lists: MAGI lists: PLANTTFDB lists: ALDEx2 lists: qBasePLUS lists: RefGenes lists: HTqPCR lists: BestKeeper lists: NanoStringNorm lists: NormFinder lists: NormqPCR lists: PolymiRTS lists: PPDB: Plant Promoter Database lists: ddCt lists: GEOSS lists: PReMod lists: EasyqpcR lists: NanoStriDE lists: GBSA lists: LaSSO lists: NAPPA lists: nSolver Analysis Software lists: MAGENTA lists: MetABEL lists: ProNIT lists: genomation lists: metagen lists: BMIQ lists: FadE lists: metaphor lists: SWAN lists: PROSITE lists: Parseq lists: qPrimerDepot lists: Bpipe lists: Nestly lists: Snakemake lists: SNAPE-pooled lists: NGSANE lists: jmzTab lists: JISTIC lists: Savant lists: MetaSKAT lists: Human Variome Project lists: PoPoolation lists: RefSeq lists: MultiPhen lists: RegulonDB lists: MF-GE lists: PheWAS R Package lists: EBSeq lists: MSMS lists: RAREMETAL lists: RevMan lists: GEPAT lists: Polyester lists: SET lists: J-Express lists: UEA sRNA toolkit lists: Osprey lists: RINS lists: PyroBayes lists: PEAR lists: JATAC lists: SeqExpress lists: Quantitative Enrichment of Sequence Tags lists: Pash 3.0 lists: Factorbook lists: FlyTF.org lists: My Cancer Genome lists: Pathosystems Resource Integration Center lists: MSG lists: InsertionMapper lists: PubMed Central lists: GeneCommittee lists: INMEX lists: TagDust lists: PASS-bis lists: HLASeq lists: FIDEA lists: EGAPP lists: DCTD lists: Hapmix lists: BamView lists: PerM lists: Mercury lists: CDP lists: CB-Commander lists: BSRD lists: DER Finder lists: Artemis: Genome Browser and Annotation Tool lists: PeaKDEck lists: PubChem lists: Babel lists: bcbio-nextgen lists: SIDER lists: EpiGRAPH lists: DRUT lists: Ancestrymap lists: VIROME lists: Vanator lists: FACIL lists: Velvet-SC lists: SNiPer-HD lists: Squeezambler lists: UniGene lists: SCPD - Saccharomyces cerevisiae promoter database lists: GASSST lists: SnoopCGH lists: Taverna lists: PASHA lists: miRDeepFinder lists: STAR lists: Spanki lists: VAMPS lists: Basic OligoNucleotide Design lists: Tree and reticulogram REConstruction lists: ACT: Artemis Comparison Tool lists: SPInDel lists: Kdetrees lists: tree editor lists: Genomedata lists: BioDiscovery Nexus Copy Number lists: TETRA lists: MetaCluster-TA lists: DELLY lists: QuickGO lists: TAIR lists: CompostBin lists: Nonpareil lists: BioPig lists: LMAT lists: AbundanceBin lists: TaxSOM lists: NuChart lists: ProViDE lists: UnifiedGenotyper lists: SOrt-ITEMS lists: RAIphy lists: Human DNA Polymerase Gamma Mutation Database lists: Pfam lists: Distributed String Mining Framework lists: Pplacer lists: deStruct lists: Phymm and PhymmBL lists: USeq lists: NucPosSimulator lists: NBC lists: SVMerge lists: MLTreeMap lists: SVseq lists: SEQanswers lists: PRISM - Pair Read Informed Split Mapper lists: miRNAKey lists: MG-RAST lists: Information Hyperlinked Over Proteins lists: PubMed lists: MetaPhyler lists: MARTA lists: NCBI BioSample lists: BioSample Database at EBI lists: DiScRIBinATE lists: VariationHunter lists: NCBI BLAST lists: IBIS: Inferred Biomolecular Interactions Server lists: NCBI Sequence Read Archive (SRA) lists: MetaPhlAn lists: Classifier for Metagenomic Sequences lists: MapAl lists: European Genome phenome Archive lists: TemplateFilter lists: Minia lists: MiTCR lists: M-pick lists: CARMA lists: SLIQ lists: DNAPlotter lists: AmphoraNet lists: UPARSE lists: SOPRA lists: ESPRIT-Tree lists: HPC-CLUST lists: mirWIP lists: SSPACE lists: GoMapMan lists: G-BLASTN lists: SINA lists: Bambus lists: AGORA lists: GRASS lists: MIP Scaffolder lists: Scarpa lists: MBCluster.Seq lists: cortex var lists: Flux Simulator lists: BEERS lists: SNPeffect lists: MMAPPR lists: Cloudbreak lists: comrad lists: qSNP lists: SomaticIndelDetector lists: SomaticSniper lists: aldex lists: UnoSeq lists: Traph lists: RNA-SeQC lists: PoPoolation TE lists: RetroSeq lists: T-lex lists: SLIDE lists: VFS lists: Project HOPE lists: PANTHER Evolutionary analysis of coding SNPs lists: rQuant lists: Naturejobs lists: jobs.ac.uk lists: ASOoViR lists: RNA-eXpress lists: MethPipe lists: AnnTools lists: AVIA lists: CandiSNPer lists: CHAoS lists: COVA lists: methylKit lists: dbNSFP lists: GESND lists: VAGrENT lists: Human Splicing Finder lists: NGS-SNP lists: Oncotator lists: PHAge Search Tool lists: SCAN lists: SeqAnt lists: SNPdat lists: ORMAN lists: FRCbam lists: SNPdbe lists: SnpEff lists: SNPnexus lists: SPOT - Biological prioritization after a SNP association study lists: VARIANT lists: ABSOLUTE lists: ExPANdS lists: HIVCD lists: PathSeq lists: READSCAN lists: VirusFinder lists: VirusSeq lists: PredictHaplo lists: QuRe lists: ShoRAH lists: V-Phaser 2 lists: NSMAP lists: FlowSim lists: SimRare lists: SAMtools/BCFtools lists: MiTie lists: GeneTalk lists: iReckon lists: Genomic Datasharing lists: IsoformEx lists: IQSeq lists: ERANGE lists: FusionMap lists: Bioinformatics(at)school lists: PhenoMan lists: Models of SHM Targeting and Substitution lists: AGE lists: Breakpointer lists: CLEVER Toolkit lists: Clippers lists: CREST lists: Indelocator lists: GASVPro lists: Hydra lists: inGAP lists: VelociMapper lists: PEMer lists: SPLITREAD lists: SpliceSeq lists: Scripture lists: Omicsoft Sequence Aligner lists: SOAPindel lists: G-Mo.R-Se lists: SEECER lists: RSeQC lists: SeqWare lists: CloVR lists: PolySearch lists: MiRPara lists: PIE the search lists: miRdSNP lists: Hmmer lists: MuGeX lists: SysCall lists: KGGSeq lists: MycoCosm lists: EBIMed lists: HighWire lists: Coremine Medical lists: Assembly Likelihood Estimator lists: CoPub lists: ABS filter lists: NCBO Annotator lists: CHANCE lists: phantompeakqualtools lists: CoIN lists: SwissRegulon lists: becas lists: GEM lists: Anne O'Tate lists: (at)Note lists: PeakSeq lists: FaBox lists: CoverageCalculator lists: Spliceman lists: Yabi lists: footprintDB lists: MolBioLib lists: Moa lists: PRISM (Stanford database) lists: Knime4Bio lists: Ergatis lists: bioKepler lists: Platypus lists: PING lists: Binding and Expression Target Analysis lists: BioExtract lists: Bio-Linux lists: NeuroLex lists: ChEA lists: ChIPBase lists: CistromeFinder lists: pyDNase lists: hmChIP lists: HOCOMOCO lists: PAZAR lists: TFinDIT lists: AtProbe lists: DATFAP lists: StSNP lists: SolexaQA lists: TOBFAC lists: MapNext lists: BSeQC lists: SKIPPY lists: SAMStat lists: QC-Chain lists: Bis-SNP lists: Bisulfighter lists: CpG MPs lists: CyMATE lists: GobyWeb lists: Kismeth lists: MethylExtract lists: MethylViewer lists: MLML lists: MSC lists: PRINSEQ lists: NGSQC lists: NGS QC Toolkit lists: NextClip lists: Geneious Microsatellite Plugin lists: DistMap lists: PRIMEGENS lists: VDJ lists: Bowtie lists: CASHX lists: CUSHAW lists: CUSHAW2-GPU lists: GNUMAP lists: GSNAP lists: Kraken lists: Maq lists: MOSAIK lists: mrFAST lists: NextGenMap lists: ngsTools lists: PASS lists: Jellyfish lists: TIGRFAMS lists: Segemehl lists: SeqMap lists: SHRiMP lists: WHAM lists: SMALT lists: Scalable Nucleotide Alignment Program lists: SOAP3 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lists: QUASR lists: simhtsd lists: 1000 Genomes: A Deep Catalog of Human Genetic Variation lists: GBrowse lists: seqbias lists: EagleView lists: HIA lists: qrqc lists: Genomes Unzipped lists: eXpress lists: ArtificialFastqGenerator lists: BarraCUDA lists: RazerS lists: Therapeutic Target Database lists: YeTFaSCo lists: PrimerBank lists: MORGAN lists: CROP lists: MeDUSA lists: Arabidopsis Gene Regulatory Information Server lists: SimSeq lists: MetMap lists: MIGen lists: eDMR lists: ProDom lists: BAMStats lists: CD-HIT-OTU lists: microRNA.org lists: Database of Genomic Variants lists: DeconSeq lists: Psort lists: Kinetic Data of Bio-molecular Interaction lists: PRODORIC lists: Database of Poplar Transcription Factors lists: BioRAT lists: Database of Arabidopsis Transcription Factors lists: RTPrimerDB- The Real-Time PCR and Probe Database lists: Pripper lists: COG lists: Yeast Intron Database lists: QDMR lists: Haldanes Sieve lists: Kevin's GATTACA World lists: Next-Gen Sequencing lists: 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HapFABIA lists: Relate lists: Pedigree-Draw lists: Pedimap lists: Phylogeny Programs lists: NHLBI Grand Opportunity Exome Sequencing Project lists: PhenCode lists: SNP and indel Imputability lists: draw-sneakpeek lists: GensearchNGS lists: HugeSeq lists: MutFinder lists: RTG Variant lists: reseqtools lists: SIMPLEX lists: TREAT lists: WEP lists: breseq lists: SVDetect lists: CEQer lists: CONTRA lists: ExomeCNV lists: CNAnorm lists: CNAseg lists: CnD lists: CNValidator lists: CNVer lists: CNVnator lists: Control-FREEC lists: JointSLM lists: readDepth lists: rSW-seq lists: SegSeq lists: CoRAL - Classification of RNAs by Analysis of Length lists: miRDeep lists: miREval lists: miRExpress lists: miRspring lists: omiRas lists: ShortStack lists: tRNAscan-SE lists: RNAsnp lists: BCmicrO lists: C-mii lists: DIANA-LncBase lists: TarBase lists: HOCTAR lists: SICER lists: MapSplice lists: TargetScan lists: MicroCosm Targets lists: MicroMUMMIE lists: miRDB lists: miRNA lists: miRNAminer lists: 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Pathway Analysis lists: Roadmap Epigenomics Project lists: PEER lists: KEGG lists: Antibodypedia lists: AcroMine lists: g:Profiler lists: HighWire Press lists: Biometric Research Branch: ArrayTools lists: R Project for Statistical Computing lists: Nu-OSCAR lists: Pedigree-Draw lists: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis lists: ChIP-Atlas lists: ProLinks Database of Functional Linkages lists: Myrna lists: lilikoi lists: GOTrack lists: Ximmer lists: NAT/NCS2 Hound lists: VoxBlast lists: Splicing Express lists: RNA22 lists: miRWalk lists: miRmap lists: AbundantOTU+ lists: MutaGene lists: VecScreen lists: NMRProcFlow lists: Attie Lab Diabetes Database lists: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS lists: XYalign lists: fermi lists: metaPocket lists: DoG picker lists: TiltPicker lists: NeuroAnatomy Toolbox lists: MAxEntScan lists: MetaNeighbor lists: OmicsNet lists: Discovar assembler lists: Supernova assembler lists: Epik lists: Ligprep lists: PathwayMatcher lists: EMAN lists: Geno2MP lists: duphold lists: ConsensusClusterPlus lists: EpiFactors lists: fastp lists: NanoFilt lists: Heatmapper lists: Nuclear Hormone Receptor Scan lists: Metacell lists: OmicsSIMLA lists: ScaffMatch lists: MITE-Tracker lists: PCAGO lists: BinPacker lists: Bridger lists: RaceID lists: PRSice lists: cwl-metrics lists: mzStudio lists: OrthoFinder lists: SwiftOrtho lists: ClustVis lists: CWL-Airflow lists: CytExpert Software lists: Computational Suite for Bioinformaticians and Biologists lists: WTDBG lists: prank lists: MACS lists: NeuroAnatomy Toolbox lists: CentroidFold lists: pKiss lists: BIDS Validator lists: PILER lists: trimAl lists: NOVOPlasty lists: GeSeq lists: Diffusion Toolkit lists: PathwayNet lists: miRTarBase lists: CLC Genomics Workbench lists: PyNWB lists: FastProject lists: DiseaseMeth lists: WormAtlas lists: GeneATLAS lists: immuneXpresso lists: BioAssay Express lists: ChemRICH lists: TransDecoder lists: GADMA lists: Alien-hunter lists: ALTER lists: AMAP lists: Anfo lists: Aragorn lists: Arden lists: Ariba lists: Augustus lists: Avogadro lists: Axe lists: Baitfisher lists: BALLView lists: Bamtools lists: Barrnap lists: BEAST lists: BioPerl lists: bioSyntax lists: Bio-tradis lists: BOXSHADE 3.21 lists: Canu lists: Cassiopee lists: Cdbfasta lists: CD-HIT lists: Circlator lists: Clearcut lists: Clonalframe lists: ClonalOrigin lists: Clustal W2 lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: Concavity lists: Cufflinks lists: cwltool lists: DIAMOND lists: DISULFIND lists: Database of Secondary Structure Assignments lists: Eigensoft lists: EMBOSS lists: ESTScan lists: FASTLINK lists: FastQC lists: FastTree lists: FigTree lists: Fsm-lite lists: Gamgi lists: Genome BioInformatics Research Lab - gff2ps lists: Ghemical lists: GIIRA lists: GROMACS lists: Gwyddion lists: Bioinformatics Toolkit lists: PyMOL lists: Biopython lists: PRESTO: Genetic Association Analysis Software lists: CummeRbund lists: ProtTest lists: Prokka lists: Computational Structural Biology Toolbox lists: LEfSe lists: jModelTest lists: khmer lists: Atac lists: LAMARC lists: FreeContact lists: libRoadRunner lists: TFBS lists: MicrobiomeUtilities lists: MINIMAC lists: MultiQC lists: Nanopolish lists: IgBLAST lists: PHYLIP lists: PhyML lists: Pilon lists: ADEGENET lists: phytools lists: R/QTL lists: RDKit: Open-Source Cheminformatics Software lists: RepeatMasker lists: SeaView lists: SEER lists: Seq-Gen lists: StringTie lists: THESIAS lists: Transterm lists: Vascular Modeling Toolkit lists: Aegean lists: andi lists: Bandage lists: Eagle lists: BioJava Project lists: Bio++ lists: BRAKER lists: Bustools lists: Centrifuge Classifier lists: ChromHMM lists: DeepNano lists: Ecopcr lists: Edtsurf lists: E-mem lists: Examl lists: Falcon lists: Fastaq lists: Fastml lists: Fastqtl lists: FSA lists: GARLI lists: Garlic lists: gdpc lists: GenomeTools lists: Gentle lists: Gff2aplot lists: gffread lists: GraPhlAn lists: Gubbins lists: Harvest-tools lists: HiLive lists: Hinge lists: HyPhy lists: Indelible lists: IQ TREE lists: Fastahack lists: Mash lists: MEGAHIT lists: Minimap2 lists: mosdepth lists: MUMmer lists: OptiType lists: Phyutility lists: Porechop lists: QIIME2 lists: Racon lists: Phangorn lists: pheatmap lists: Recognition of Errors in Assemblies using Paired Reads lists: RELION lists: Roary lists: Salmon lists: Scoary lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Seqtk lists: Short Read Sequence Typing for Bacterial Pathogens lists: Vmatch lists: ABACAS lists: AceDB lists: tRNAscan-SE lists: Antibody Resource Page is related to: COnsensus-DEgenerate Hybride Oligonucleotide Primers is related to: Classifier for Metagenomic Sequences is related to: Pedigree-Draw is related to: CAZy- Carbohydrate Active Enzyme is related to: PolyPhen: Polymorphism Phenotyping is related to: BioRAT is related to: dChip Software is related to: Rat Genome Database (RGD) is related to: Comparative Toxicogenomics Database (CTD) is related to: VISTA Enhancer Browser is related to: affy		PMID:25024350	THIS RESOURCE IS NO LONGER IN SERVICE	nlx_155571, r3d100012426	https://doi.org/10.17616/R3PJ3N	http://omictools.com/	SCR_002250	genOMIC tools	2026-08-10 09:31:40	34
Kyushu University; Fukuoka; Japan Resource Report Resource Website 1+ mentions	Kyushu University; Fukuoka; Japan (RRID:SCR_004149)		university	Japanese national university located in Fukuoka, in the island of Kyushu.		is parent organization of: Signaling Pathway Database is parent organization of: Kyushu University Definitive Haplotype Database is parent organization of: ChIP-Atlas				nlx_23378, Wikidata:Q1188786, ISNI:0000 0001 2242 4849, grid.177174.3, Crossref funder ID:501100004096	https://ror.org/00p4k0j84		SCR_004149		2026-08-08 11:58:16	1
NBDC - National Bioscience Database Center Resource Report Resource Website 1+ mentions	NBDC - National Bioscience Database Center (RRID:SCR_000814)	NBDC	data or information resource, portal, database, organization portal	The National Bioscience Database Center (NBDC) intends to integrate all databases for life sciences in Japan, by linking each database with expediency to maximize convenience and make the entire system more user-friendly. We aim to focus our attention on the needs of the users of these databases who have all too often been neglected in the past, rather than the needs of the people tasked with the creation of databases. It is important to note that we will continue to honor the independent integrity of each database that will contribute to our endeavor, as we are fully aware that each database was originally crafted for specific purposes and divergent goals. Services: * Database Catalog - A catalog of life science related databases constructed in Japan that are also available in English. Information such as URL, status of the database site (active vs. inactive), database provider, type of data and subjects of the study are contained for each database record. * Life Science Database Cross Search - A service for simultaneous searching across scattered life-science databases, ranging from molecular data to patents and literature. * Life Science Database Archive - maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata in a unified format, and to access and download the datasets with clear terms of use. * Taxonomy Icon - A collection of icons (illustrations) of biological species that is free to use and distribute. There are more than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia. * GenLibi (Gene Linker to bibliography) - an integrated database of human, mouse and rat genes that includes automatically integrated gene, protein, polymorphism, pathway, phenotype, ortholog/protein sequence information, and manually curated gene function and gene-related or co-occurred Disease/Phenotype and bibliography information. * Allie - A search service for abbreviations and long forms utilized in life sciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader's expertise. * inMeXes - A search service for English expressions (multiple words) that appear no less than 10 times in PubMed/MEDLINE titles or abstracts. In addition, you can easily access the sentences where the expression was used or other related information by clicking one of the search results. * HOWDY - (Human Organized Whole genome Database) is a database system for retrieving human genome information from 14 public databases by using official symbols and aliases. The information is daily updated by extracting data automatically from the genetic databases and shown with all data having the identifiers in common and linking to one another. * MDeR (the MetaData Element Repository in life sciences) - a web-based tool designed to let you search, compare and view Data Elements. MDeR is based on the ISO/IEC 11179 Part3 (Registry metamodel and basic attributes). * Human Genome Variation Database - A database for accumulating all kinds of human genome variations detected by various experimental techniques. * MEDALS - A portal site that provides information about databases, analysis tools, and the relevant projects, that were conducted with the financial support from the Ministry of Economy, Trade and Industry of Japan.	life science, research, database, catalog, tool, gene, service, molecule, patent, literature, taxonomy, image, bacteria, fungus, protist, plant, animal, human, mouse, rat, gene, protein, polymorphism, pathway, phenotype, ortholog, protein sequence, gene function, disease, phenotype, bibliography, english expression, human genome, genome, human genome variation, variation, analysis tool	has parent organization: Japan Science and Technology Agency is parent organization of: Human Variation DB is parent organization of: Japanese Genotype-phenotype Archive (JGA) is parent organization of: ChIP-Atlas	Japan Science and Technology Agency			nlx_151485			SCR_000814	National Bioscience Database Center, National Bioscience Database Center (NBDC)	2026-08-11 09:40:13	3

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