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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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CBFBIRN Resource Report Resource Website 1+ mentions |
CBFBIRN (RRID:SCR_009543) | CBFBIRN | data or information resource, data repository, data set, service resource, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users. |
java, javascript, matlab, magnetic resonance, os independent, web environment, arterial spin labeling, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cerebral Blood Flow Database and Analysis Pipeline has parent organization: University of California at San Diego; California; USA |
NIH | PMID:24151465 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155722 | http://www.nitrc.org/projects/cbfbirn | SCR_009543 | SciCrunch Registry | Cerebral Blood Flow Biomedical Informatics Research Network | 2026-11-07 11:56:52 | 3 | ||||
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Pep2TCR Resource Report Resource Website 1+ mentions |
Pep2TCR (RRID:SCR_024721) | data access protocol, software resource, source code, web service | Web tool for CD4 TCR specificity prediction and biology applications. Used for accurate prediction of CD4 T cell receptor binding specificity through transfer learning and ensemble approach. Repository comprises codes of Pep2TCR, providing comprehensive guidance for researchers interested in Pep2TCR. | CD4 TCR specificity prediction, deep learning, transfer learning, ensemble learning, neoantigen, CD4+ T cell | Free, Available for download, Freely available | https://hub.docker.com/repository/docker/liuxslab/pep2tcr, http://pep2tcr.liuxslab.com | SCR_024721 | SciCrunch Registry | 2026-11-07 12:06:00 | 1 | ||||||||||
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bio.tools Resource Report Resource Website 10+ mentions |
bio.tools (RRID:SCR_014695) | catalog, data or information resource, database, software repository, software resource | 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 lists: Drybench lists: ProtBed lists: SwapSeq 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 |
Danish Ministry of Higher Education and Science ; European Union Horizon 2020 ELIXIR-EXCELERATE grant 676559 |
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 | SciCrunch Registry | 2026-11-07 11:57:54 | 29 | |||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | d spatial image, data or information resource, data repository, database, image collection, service resource, storage service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | SciCrunch Registry | Organelle DB: A Database of Organelles and Protein Complexes | 2026-11-07 11:56:27 | 7 | |||||
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Animal Genome Size Database Resource Report Resource Website 100+ mentions |
Animal Genome Size Database (RRID:SCR_007551) | Genomesize | catalog, data or information resource, data repository, database, service resource, storage service resource | Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff. | genome size, haploid dna, non-vertebrate, vertebrate, genome structure, comparative biodiversity, sequencing, genome, genomic, FASEB list | has parent organization: University of Guelph; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada | PMID:17090588 | Data taken from the database must not be reproduced in published lists, Online databases, Or other such formats, Nor redistributed without permission. The information is provided solely for personal and academic use., Please cite, The community can contribute to this resource | nif-0000-02548, r3d100012517 | https://doi.org/10.17616/R3R782, https://doi.org/10.17616/R3R782 | SCR_007551 | SciCrunch Registry | 2026-11-07 11:56:26 | 190 | |||||
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PGN Resource Report Resource Website |
PGN (RRID:SCR_004559) | PGN | analysis service resource, data analysis service, data or information resource, data repository, data set, database, production service resource, service resource, storage service resource | Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future. | expressed sequence tag, genomics, functional annotation, blast, sequencing, chromatogram | has parent organization: Cornell University; New York; USA | NSF DBI-9872617; NSF DBI-0115684 |
nlx_55223 | SCR_004559 | SciCrunch Registry | PGN - Plant Genome Network, Plant Genome Network | 2026-11-07 11:55:32 | 0 | |||||||
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Leiden Open Variation Database Resource Report Resource Website 100+ mentions |
Leiden Open Variation Database (RRID:SCR_006566) | LOVD | data or information resource, data processing software, data repository, data storage software, database, service resource, software application, software resource, storage service resource | Freely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats. | genetic variation, genomic variant, gene, transcript, disease, next generation sequencing, dna variation, variant, clinical, screening, locus, phenotype, sequence variation, allelic variant, data sharing, FASEB list |
is listed by: OMICtools has parent organization: Leiden University; Leiden; Netherlands |
European Union FP7 GEN2PHEN 200754 | PMID:21520333 PMID:15977173 |
The community can contribute to this resource, Clearance to contribute required, GNU General Public License, Acknowledgement requested | nif-0000-02998, OMICS_00275, r3d100011905 | https://doi.org/10.17616/R3993T | SCR_006566 | SciCrunch Registry | Leiden Open Variation Database (LOVD) | 2026-11-07 11:56:11 | 315 | ||||
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Global Proteome Machine Database (GPM DB) Resource Report Resource Website 100+ mentions |
Global Proteome Machine Database (GPM DB) (RRID:SCR_006617) | The GPM | data analysis software, data or information resource, data processing software, data repository, database, service resource, software application, software resource, storage service resource | The Global Proteome Machine Organization was set up so that scientists involved in proteomics using tandem mass spectrometry could use that data to analyze proteomes. The projects supported by the GPMO have been selected to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists. | mass spectrometry, pattern, peptide, protein, proteome, scientist, spectra, tandem, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
r3d100010883, nif-0000-10455 | https://www.thegpm.org/GPMDB/index.html, https://researchdata.ands.org.au/gpm-global-proteome-machine-database/11342, https://doi.org/10.17616/R30C90 | SCR_006617 | SciCrunch Registry | GPM, The Global Proteome Machine Organization: Proteomics Database and Open Source Software, Global Proteome Machine Database, GPM DB, The Global Proteome Machine Database, The Global Proteome Machine, Global Proteome Machine Database (GPM DB), The Global Proteome Machine Organization | 2026-11-07 11:56:12 | 282 | |||||||
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GeoStrat Resource Report Resource Website |
GeoStrat (RRID:SCR_009428) | GeoStrat | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29,2019. Sedimentary geologic and biostratigraphic data. | sediment, geology, biostratigraphy | is listed by: CINERGI | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154709 | SCR_009428 | SciCrunch Registry | 2026-11-07 11:56:42 | 0 | ||||||||
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dbVar Resource Report Resource Website 100+ mentions |
dbVar (RRID:SCR_003219) | dbVar | data or information resource, data repository, database, service resource, storage service resource | Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. | structure, variation, structural variation, genetics, insertion, deletion, copy number variant, inversion, translocation, genomic imbalance, genotype, gene expression, dna, genomics, phenotype, genetic code |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is related to: Database of Genomic Variants Archive (DGVa) is related to: Database of Genomic Variants has parent organization: NCBI |
PMID:23193291 | Free, Freely available | nlx_157217, r3d100010758 | https://doi.org/10.17616/R3V610 | SCR_003219 | SciCrunch Registry | dbVar, Database of Genomic Structural Variation, NCBI dbVar | 2026-11-07 11:54:57 | 198 | |||||
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PhosPhAt Resource Report Resource Website 50+ mentions |
PhosPhAt (RRID:SCR_003332) | PhosPhAt | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database containing information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor. Users and researchers are encouraged to assist in keeping the database current by submitting either published data or unpublished data (MS/MS data required). | phosphorylation, peptide, function, mass spectrometry, kinase, serine, threonine, tyrosine, phosphoprotein, phosphopeptide, tryptic phosphopeptide, serine phosphosite, threonine phosphosite, tyrosine phosphosite, FASEB list | has parent organization: University of Hohenheim; Baden-Wurttemberg; Germany | PMID:23172287 PMID:19880383 PMID:17984086 |
Free, Freely available | nif-0000-03277 | http://phosphat.mpimp-golm.mpg.de/app.html | SCR_003332 | SciCrunch Registry | Arabidopsis Protein Phosphorylation Site Database | 2026-11-07 11:54:55 | 62 | |||||
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VAMPS Resource Report Resource Website 10+ mentions |
VAMPS (RRID:SCR_004483) | VAMPS | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally. |
is listed by: OMICtools has parent organization: Marine Biological Laboratory |
Alfred P. Sloan Foundation ; NSF ; NASA Astrobiology Institute |
PMID:24499292 | Public, The community can contribute to this resource | OMICS_01501 | SCR_004483 | SciCrunch Registry | VAMPS Project, Visualization and Analysis of Microbial Population Structure | 2026-11-07 11:55:21 | 28 | ||||||
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Functional Anatomy of the Cerebro-Cerebellar System (FACCS) Resource Report Resource Website |
Functional Anatomy of the Cerebro-Cerebellar System (FACCS) (RRID:SCR_001661) | FACCS | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Public neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway. | axonal tracer, axon tracing, brain, cerebellum, cerebral cortex, cerebro-cerebellar function, cerebro-cerebellar structure, cerebro-cerebellar system, injection, injection site, labeled cells, labeled fibers, pontine nuclear complex, pontine nuclei, video, cerebellar cortex | has parent organization: University of Oslo; Oslo; Norway | Research Council of Norway ; Centre for Molecular Biology and Neuroscience ; European Union |
PMID:17426352 PMID:16344144 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02317 | SCR_001661 | SciCrunch Registry | Functional Anatomy of the Cerebro-Cerebellar System | 2026-11-07 11:54:23 | 0 | |||||
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Oregon Brain Bank Resource Report Resource Website |
Oregon Brain Bank (RRID:SCR_013085) | biomaterial supply resource, material resource | Brain bank that harvests, banks and disperses postmortem tissue for use in brain and medical research. It also provides neuropathologic diagnoses of organic dementia in a cohort of NIH sponsored research subjects. The bank includes tissue primarily from patients with Alzheimer's but also includes Huntington's, Parkinson's, and other disorders. | neurodegenerative research, postmortem, tissue, neurodegenerative, neurodegenerative disease, alzheimer's disease, huntington's disease, parkinson's disease, amyotrophic lateral sclerosis, multiple sclerosis, control, tissue, brain tissue, left hemisphere, right hemisphere, white matter, deep gray structure, brainstem, cerebellum, spinal cord, late adult human, flash frozen, formalin-fixed, stained, brain bank, research, medical |
is listed by: One Mind Biospecimen Bank Listing is related to: Layton Center Clinical Data Resources has parent organization: Oregon Health and Science University; Oregon; USA |
Alzheimer's disease, Huntington's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Dementia, Neurodegenerative disease, Aging | According to established protocols, For use in neurodegenerative research | nlx_35532 | SCR_013085 | SciCrunch Registry | Oregon Brain Bank: Human tissue repository for neurodegenerative research studies | 2026-11-07 12:03:50 | 0 | |||||||
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Layton Center Biomarkers and Genetics Resource Report Resource Website |
Layton Center Biomarkers and Genetics (RRID:SCR_008824) | Layton Biomarkers and Genetics | biomaterial supply resource, material resource | A center that works with the Oregon Alzheimer's Disease Center's Data Core, and collects and stores tissue samples, family history and genotype data of various populations. These include samples and data from subjects from the following sources: OADC clinical studies, the Oregon Brain Aging Study, the Community Brain Donor Program, the Preventing Cognitive Decline with Alternative Therapies program (informally called the Dementia Prevention Study or DPS), the African American Dementia and Aging Project, and the Klamath Exceptional Aging Project. The collected data samples include genomic DNA, lymphoblast cell lines, genome-wide and candidate region SNP marker data, APOE, AD candidate gene markers. | genomic dna, lymphoblast cell line, plasma, dna, cell line, lymphoblast, dementia, late adult human, normal, alzheimer's disease, clinical data, genotype data, genotype, clinical, family history |
is listed by: One Mind Biospecimen Bank Listing has parent organization: OHSU Layton Aging and Alzheimer's Disease Center |
Aging, Dementia, Alzheimer's disease | NIA P30 AG08017 | Researchers must fill out request forms | nlx_144448 | SCR_008824 | SciCrunch Registry | Layton Aging and Alzheimers Disease Center Biomarkers and Genetics, Layton Center Biomarkers and Genetics | 2026-11-07 12:03:19 | 0 | |||||
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Nanotomy Resource Report Resource Website 10+ mentions |
Nanotomy (RRID:SCR_018565) | data or information resource, data repository, data set, database, image collection, service resource, storage service resource | Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes. | Large scale, electron microscopy, data set, Human Type 1 Diabetes, image collection |
is related to: Golddigger has parent organization: University of Groningen; Groningen; Netherlands |
Type 1 diabetes, Diabetes | PMID:32424134 | Free, Freely available | SCR_020961 | SCR_018565 | SciCrunch Registry | nano-anatomy, Anatomy at nanoscale, nanotomy | 2026-11-07 11:59:04 | 30 | ||||||
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Rat Hippocampus Atlas Resource Report Resource Website 1+ mentions |
Rat Hippocampus Atlas (RRID:SCR_005552) | Rat Hippocampus Atlas | atlas, data or information resource, reference atlas | An interactive reference atlas providing a systematic overview of cyto- and chemoarchectonical features of the hippocampus proper, fasciola, and associated parahippocampal cortices. This atlas system has been developed to serve the need to integrate detailed descriptions of structures and criteria defining boundaries and atlas images in which the underlying histological features can be explored. Features * Alphabetical and hierarchical overview of 18 hippocampal structures * Detailed, illustrated descriptions of 63 boundaries * Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin * Triple image viewer in which differently stained neighboring sections can be interactively compared * Graphical overlay of substructures based on described boundary criteria * Bidirectional links between structure descriptions and image repository The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin. The system is intended for researchers working in the field, as well as students interested in this brain region. The atlas is accessed through the structure index or image viewer. Re-use of data from this repository is allowed provided that reference is given to the publication. | rat, hippocampus, adult rat, long evans rat, hippocampus proper, fasciola, parahippocampal cortex, neuroanatomy, histology |
is related to: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat has parent organization: University of Oslo; Oslo; Norway |
University of Oslo; Oslo; Norway ; Research Council of Norway ; International Neuroinformatics Coordinating Facility ; Norwegian Node |
PMID:21519393 | nlx_144643 | SCR_005552 | SciCrunch Registry | 2026-11-07 12:01:27 | 4 | |||||||
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Chromosome 7 Annotation Project Resource Report Resource Website 10+ mentions |
Chromosome 7 Annotation Project (RRID:SCR_007134) | Chromosome 7 Annotation Project | data or information resource, data repository, database, service resource, storage service resource | Database containing the DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented; the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as unpublished data. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. The objective of this project is to generate a comprehensive description of human chromosome 7 to facilitate biological discovery, disease gene research and medical genetic applications. There are over 360 disease-associated genes or loci on chromosome 7. A major challenge ahead will be to represent chromosome alterations, variants, and polymorphisms and their related phenotypes (or lack thereof), in an accessible way. In addition to being a primary data source, this site serves as a weighing station for testing community ideas and information to produce highly curated data to be submitted to other databases such as NCBI, Ensembl, and UCSC. Therefore, any useful data submitted will be curated and shown in this database. All Chromosome 7 genomic clones (cosmids, BACs, YACs) listed in GBrowser and in other data tables are freely distributed. | duplication, gene expression, family, fish, gene, gene annotation, genome, breakpoint, chromosome, chromosome 7, clinical, deletion, disease, dna sequence, human, insertion, inversion, polymorphism, rearrangement, segmental duplication, snp, translocation, annotation, data analysis service, blat, cosmid, bac, yac, biomaterial supply resource, malignant, non malignant, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools |
PMID:12690205 | Free, (Genomic clones) | nif-0000-03550, biotools:chr7, r3d100012136 | https://bio.tools/chr7, https://doi.org/10.17616/R3VP9V | SCR_007134 | SciCrunch Registry | The Chromosome 7 Annotation Project, Chromosome 7 Annotation Project | 2026-11-07 11:56:19 | 13 | |||||
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Framingham Heart Study Resource Report Resource Website 100+ mentions |
Framingham Heart Study (RRID:SCR_008963) | FHS | biomaterial supply resource, material resource | A longitudinal, epidemiologic study to identify the common risk factors or characteristics that contribute to cardiovascular disease by following its development over a long period of time in a large group of participants who had not yet developed overt symptoms or suffered a heart attack or stroke. Since that time the FHS has studied three generations of participants resulting in biological specimens and data from nearly 15,000 participants. Since 1994, two groups from minority populations, including related individuals have been added to the FHS. FHS welcomes proposals from outside investigators for data and biospecimens. The researchers recruited 5,209 men and women between the ages of 30 and 62 from the town of Framingham, Massachusetts, and began the first round of extensive physical examinations and lifestyle interviews that they would later analyze for common patterns related to CVD development. Since 1948, the subjects have continued to return to the study every two years for a detailed medical history, physical examination, and laboratory tests, and in 1971, the Study enrolled a second generation - 5,124 of the original participants'''' adult children and their spouses - to participate in similar examinations. In 1994, the need to establish a new study reflecting a more diverse community of Framingham was recognized, and the first Omni cohort of the Framingham Heart Study was enrolled. In April 2002 the Study entered a new phase, the enrollment of a third generation of participants, the grandchildren of the Original Cohort. In 2003, a second group of Omni participants was enrolled. Over the years, careful monitoring of the Framingham Study population has led to the identification of major CVD risk factors, as well as valuable information on the effects of these factors such as blood pressure, blood triglyceride and cholesterol levels, age, gender, and psychosocial issues. Risk factors for other physiological conditions such as dementia have been and continue to be investigated. In addition, the relationships between physical traits and genetic patterns are being studied. FHS clinical and research data is stored in the dbGaP and NHLBI Repository repositories and may be accessed by application. Please check the following repositories before applying for data through FHS. Investigators seeking data that is not available through dbGaP or BioLINCC or seeking biological specimens may submit a proposal through the FHS web-based research application. The FHS data repository may be accessed through this FHS website, under the For Researchers link, then Description of Data, in order to determine if and how the desired data is stored. Proposals may involve the use of existing data, the collection of new data, either directly from participants or from previously collected samples, images, or other materials (e.g., medical records). The FHS Repository also has biological specimens available for genetic and non-genetic research proposals. Specimens include urine, blood and blood products, as well as DNA. | clinical study, longitudinal study, heart, cardiac, adult human, male, female, risk factor, blood pressure, blood triglyceride, cholesterol level, age, gender, psychosocial, dementia, physical trait, genetic trait, minority, clinical, genotype, phenotype, urine, blood, blood product, dna, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) has parent organization: Boston University; Massachusetts; USA |
Cardiovascular disease, Normal, Aging | NHLBI Division of Prevention and Population Sciences | Public / Collaboration preferred: FHS welcomes proposals from outside investigators. Collaboration with FHS investigators is encouraged as it helps to maximize the scientific potential of the unique data. | nlx_151991 | SCR_008963 | SciCrunch Registry | 2026-11-07 12:03:40 | 164 | ||||||
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Standards-based Infrastructure with Distributed Resources Resource Report Resource Website |
Standards-based Infrastructure with Distributed Resources (RRID:SCR_004532) | SIDR | data or information resource, data repository, database, service resource, storage service resource | A searchable public data repository for multi-assay studies in the field of high-throughput biology. Studies are annotated and curated using ontologies and controlled vocabularies according to the recommendations of the OBO foundry (Open Biological and Biomedical Ontologies) and the NCBO bioportal. Each data set is assigned a digital object identifier (DOI) provided by DataCite. In addition, the SIDR team has developed an ISA-XML (ISA-ML) version of the ISA-TAB format and the mapping to the FuGE object model (ISA-TABtoFuGE); these improvements should facilitate further tool integration, including web services. SIDR contributes to the proof-of-concept addressing the critical success factor for data integration. The SIDR team will continue to put in place the building blocks for giving access to interoperable data through a world-wide network of national hubs in the context of the community-based ISA infrastructure. | standards-based database, metadata standard, digital object identifier, assay, high-throughput, interoperability, data sharing, standardization, multi-omics |
is listed by: 3DVC is listed by: DataCite is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FAIRsharing is related to: OBO has parent organization: Institute for Scientific and Technical Information |
Institute for Scientific and Technical Information ; Institute of Biological Sciences ; IBiSA ; Regional Council of Lorraine |
Creative Commons License, The community can contribute to this resource | nlx_52124 | SCR_004532 | SciCrunch Registry | 2026-11-07 11:55:48 | 0 |
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