Searching the RRID Resource Information Network
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | data access protocol, software application, production service resource, data processing software, data analysis software, analysis service resource, service resource, software resource, web service, data analysis service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Union ; Biotechnology and Biological Sciences Research Council ; EMBL |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html https://bio.tools/interproscan_4 |
SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-02-17 10:00:40 | 6936 | |||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | data or information resource, production service resource, analysis service resource, database, service resource, software resource, data analysis service | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-02-17 10:00:48 | 3358 | |||||
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University of Barcelona Statistics and Bioinformatics Research Group Resource Report Resource Website |
University of Barcelona Statistics and Bioinformatics Research Group (RRID:SCR_005704) | UB Statistics and Bioinformatics Research Group | data or information resource, topical portal, production service resource, analysis service resource, service resource, data analysis service, portal | The Statistics and Bioinformatics research group has as its main objectives the development of methods and tools to deal with problems appearing in the interface between Statistics and Bioinformatics. We started focusing in DNA microarrays but we are also interested in statistical methods for ''omics'' data integration and next generation sequencing (NGS). Our group collaborates with different research groups in the fields of biology and biomedicine, to whom it offers statistical support for problems which are specifically statistic in nature, such as experimental design or microarray data analysis, and also in more general aspects, such as modeling, analysis or data mining. After a first period of collaboration agreements with the Fundaci�� Vall d''Hebr��n Institut de Recerca we contributed to the creation of the Statistics and Bioinformatics Unit (UEB) which provides statistical and bioinformatical support to VHIR researchers. | statistics, bioinformatics, next generation sequencing, dna microarray, dna, microarray, biology, biomedicine, data mining, modeling, analysis | has parent organization: University of Barcelona; Barcelona; Spain | nlx_149154 | SCR_005704 | University of Barcelona Statistics Bioinformatics Research Group | 2026-02-17 10:00:37 | 0 | ||||||||
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go-moose Resource Report Resource Website |
go-moose (RRID:SCR_005666) | go-moose | data analysis software, software application, data processing software, software resource | go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, slimmer-type tool, analysis, gene ontology, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: go-perl is related to: go-db-perl has parent organization: SourceForge has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: Lawrence Berkeley National Laboratory |
Free for academic use | nlx_149189 | SCR_005666 | 2026-02-17 10:00:56 | 0 | ||||||||
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Onto-Translate Resource Report Resource Website 1+ mentions |
Onto-Translate (RRID:SCR_005725) | Onto-Translate | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool | annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | Free for academic use | nlx_149182 | SCR_005725 | 2026-02-17 10:00:56 | 3 | |||||||
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GOTaxExplorer Resource Report Resource Website |
GOTaxExplorer (RRID:SCR_005720) | GOTaxExplorer | data or information resource, production service resource, analysis service resource, database, service resource, software resource, data analysis service | GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: Pfam is related to: SMART is related to: FSST - Functional Similarity Search Tool has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network ; BMBF 016R0453; DFG KFO 129/1-1; European Union contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149179 | SCR_005720 | 2026-02-17 10:00:38 | 0 | ||||||
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Onto-Miner Resource Report Resource Website |
Onto-Miner (RRID:SCR_005722) | OM | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | Onto-Miner (OM) provides a single and convenient interface that allows the user to interrogate our databases regarding annotations of known genes. OM will return all known information about a given list of genes. Advantages of OM include the fact it allows queries with multiple genes and allows for scripting. This is unlike GenBank which uses a single gene navigation process. Scripted search of the Onto-Tools database for gene annotations. User account required. Platform: Online tool | gene, annotation, search engine, database, analysis, ontology or annotation search engine, database or data warehouse, other analysis, scripted search of the onto-tools database for gene annotations |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 PMID:17584796 |
Free for academic use | nlx_149181 | SCR_005722 | Onto-Miner (OM) | 2026-02-17 10:00:58 | 0 | ||||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | software application, image processing software, data processing software, software resource, image analysis software | A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. | ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Database is related to: Brede Wiki has parent organization: THOR Center for Neuroinformatics |
Free for academic use, Acknowledgement requested | nif-0000-00275 | SCR_006204 | 2026-02-17 10:00:47 | 1 | ||||||||
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Knime Resource Report Resource Website 500+ mentions |
Knime (RRID:SCR_006164) | KNIME | software application, workflow software, text-mining software, data processing software, software resource, software toolkit | KNIME (Konstanz Information Miner) is a user-friendly and comprehensive Open-Source data integration, processing, analysis, and exploration platform. KNIME (naim) is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualization and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. KNIME can be downloaded onto the desktop and used free of charge. KNIME products include additional functionalities such as shared repositories, authentication, remote execution, scheduling, SOA integration and a web user interface as well as world-class support. Robust big data extensions are available for distributed frameworks such as Hadoop. KNIME is used by over 3000 organizations in more than 60 countries. The modular data exploration platform, initially developed at the University of Konstanz, Germany, enables the user to visually create data flows, execute selected analysis steps, and later investigate the results through interactive views on data and models. KNIME is a proven integration platform for tools of numerous vendors due to its open and modular API. The KNIME.com product pipeline includes an Enterprise Server, Cluster Execution, Reporting solutions, and professional KNIME support subscriptions. KNIME.com also offer services such as data analysis, hands-on training and the development of customized components for KNIME. | platform, next-generation sequencing, data analysis, visualization, selection, analysis, high-throughput screening, data mining, drug discovery | has parent organization: University of Konstanz; Baden-Wurttemberg; Germany | PMID:23110532 PMID:22644661 PMID:22607449 PMID:21984761 PMID:21873641 |
nlx_151666 | SCR_006164 | Konstanz Information Miner | 2026-02-17 10:00:52 | 717 | |||||||
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Cornell University BRC Bioinformatics Core Facility Resource Report Resource Website 10+ mentions |
Cornell University BRC Bioinformatics Core Facility (RRID:SCR_021757) | service resource, access service resource, core facility | Facility provides access to high performance computing environment, BioHPC, which includes both hosted hardware and shared machines. Provides consulting and collaborations for Bioinformatics analysis and workflows. | USEDit, ABRF, bioinformatics, analysis, workflows |
is listed by: ABRF CoreMarketplace has parent organization: Cornell University; New York; USA |
ABRF_109 | https://coremarketplace.org/?FacilityID=109 | SCR_021757 | BRC Bioinformatics Facility | 2026-02-17 10:03:53 | 14 | ||||||||
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Genetic Analysis Workshop Resource Report Resource Website 10+ mentions |
Genetic Analysis Workshop (RRID:SCR_008350) | workshop, training resource | The Genetic Analysis Workshops (GAWs) are a collaborative effort among genetic epidemiologists to evaluate and compare statistical genetic methods. For each GAW, topics are chosen that are relevant to current analytical problems in genetic epidemiology, and sets of real or computer-simulated data are distributed to investigators worldwide. Results of analyses are discussed and compared at meetings held in even-numbered years. The GAWs began in 1982 were initially motivated by the development and publication of several new algorithms for statistical genetic analysis, as well as by reports in the literature in which different investigators, using different methods of analysis, had reached contradictory conclusions. The impetus was initially to determine the numerical accuracy of the algorithms, to examine the robustness of the methodologies to violations of assumptions, and finally, to compare the range of conclusions that could be drawn from a single set of data. The Workshops have evolved to include consideration of problems related to analyses of specific complex traits, but the focus has always been on analytical methods. The Workshops provide an opportunity for participants to interact in addressing methodological issues, to test novel methods on the same well-characterized data sets, to compare results and interpretations, and to discuss current problems in genetic analysis. The Workshop discussions are a forum for investigators who are evolving new methods of analysis as well as for those who wish to gain further experience with existing methods. The success of the Workshops is due at least in part to the focus on specific problems and data sets, the informality of sessions, and the requirement that everyone who attends must have made a contribution. Topics are chosen and a small group of organizers is selected by the GAW Advisory Committee. Data sets are assembled, and six or seven months before each GAW, a memo is sent to individuals on the GAW mailing list announcing the availability of the GAW data. Included with the memo is a short description of the data sets and a form for requesting data. The form contains a statement to be signed by any investigator requesting the data, acknowledging that the data are confidential and agreeing not to use them for any purpose other than the Genetic Analysis Workshop without written permission from the data provider(s). Data are distributed by the ftp or CD-ROM or, most recently, on the web, together with a more complete written description of the data sets. Investigators who wish to participate in GAW submit written contributions approximately 6-8 weeks before the Workshop. The GAW Advisory Committee reviews contributions for relevance to the GAW topics. Contributions are assembled and distributed to all participants approximately two weeks before the Workshop. Participation in the GAWs is limited to investigators who (1) submit results of their analyses for presentation at the Workshop, or (2) are data providers, invited speakers or discussants, or Workshop organizers. GAWs are held just before the meetings of the American Society of Human Genetics or the International Genetic Epidemiology Society, at a meeting site nearby. We choose a location that will encourage interaction among participants and permit an intense period of concentrated work. The proceedings of each GAW are published. Proceedings from GAW16 were published in part by Genetic Epidemiology 33(Suppl 1), S1-S110 (2009) and in part by Biomed Central (BMC Proceedings, Volume 3, Supplement 7, 2009). Sponsors: GAW is funded by the Southwest Foundation for Biomedical Research. | epidemiologist, epidemiology, genetic, algorithm, analysis, method, statistical | nif-0000-25214 | SCR_008350 | GAW | 2026-02-17 10:01:20 | 19 | ||||||||||
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Bioconductor Resource Report Resource Website 10000+ mentions |
Bioconductor (RRID:SCR_006442) | software resource, software toolkit, software repository | Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data. | catalog, analysis, genomic, metadata, comprehension, statistical, data |
lists: MSstats lists: MetaCyto lists: MetaNeighbor lists: tximport lists: clusterProfiler lists: ropls lists: FlowSOM lists: scran lists: Rsubread lists: riboSeqR lists: Biostrings lists: ConsensusClusterPlus lists: DESeq2 lists: GenomicFeatures lists: affy lists: affydata lists: Genomic Ranges lists: Goseq lists: GAGE lists: CATALYST lists: Scmap lists: Scfind lists: GenomicRanges lists: org.Rn.eg.db lists: Extending Guilt by Association by Degree lists: ggtree lists: StructuralVariantAnnotation lists: scTHI lists: EnhancedVolcano lists: DEGreport lists: variancePartition lists: biomaRt lists: MSnbase lists: ReactomePA lists: SynergyFinder lists: CiteFuse lists: fgsea lists: GSVA lists: SimFFPE lists: FilterFFPE lists: PhenStat lists: ChIPseeker lists: AUCell lists: svaNUMT lists: KEGGgraph lists: epialleleR lists: microbiome lists: Orthology.eg.db lists: org.Hs.eg.db lists: ExperimentHub lists: combi is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: SoftCite is affiliated with: RnaSeqGeneEdgeRQL is related to: asSeq is related to: Gene Ontology is related to: CRCView is related to: R Project for Statistical Computing is related to: GEO2R is related to: LIMMA is related to: VisR is related to: edgeR is related to: IMEx - The International Molecular Exchange Consortium is related to: CATALYSTLite is related to: ascend is related to: minet has parent organization: Fred Hutchinson Cancer Center is parent organization of: ncdfFlow is parent organization of: GenomicRanges is parent organization of: ReadqPCR is parent organization of: flowCL is parent organization of: flowBin is parent organization of: CorMut is parent organization of: metaSeq is parent organization of: VariantAnnotation is parent organization of: ReQON is parent organization of: timecourse is parent organization of: RmiR.Hs.miRNA is parent organization of: AffyRNADegradation is parent organization of: ArrayExpress (R) is parent organization of: GEOquery is parent organization of: MIMOSA is parent organization of: HEM is parent organization of: CNTools is parent organization of: cn.FARMS is parent organization of: Clonality is parent organization of: TransView is parent organization of: pvac is parent organization of: QUALIFIER is parent organization of: flowStats is parent organization of: rTANDEM is parent organization of: flowFlowJo is parent organization of: iASeq is parent organization of: OLINgui is parent organization of: SigFuge is parent organization of: Rdisop is parent organization of: GeneExpressionSignature is parent organization of: iBMQ is parent organization of: TDARACNE is parent organization of: flowQ is parent organization of: FlipFlop is parent organization of: RmiR is parent organization of: bsseq is parent organization of: ExomePeak is parent organization of: flowWorkspace is parent organization of: massiR is parent organization of: rbsurv is parent organization of: GeneMeta is parent organization of: MergeMaid is parent organization of: categoryCompare is parent organization of: metahdep is parent organization of: snpStats: SnpMatrix and XSnpMatrix classes and methods is parent organization of: CNVtools is parent organization of: CGEN is parent organization of: RCASPAR is parent organization of: iterativeBMAsurv is parent organization of: multtest is parent organization of: globaltest is parent organization of: MinimumDistance is parent organization of: VegaMC is parent organization of: VanillaICE is parent organization of: SNPchip is parent organization of: SMAP is parent organization of: quantsmooth is parent organization of: mBPCR is parent organization of: ITALICS is parent organization of: GenoSet is parent organization of: exomeCopy is parent organization of: CGHregions is parent organization of: CGHbase is parent organization of: beadarraySNP is parent organization of: GLAD is parent organization of: methylMnM is parent organization of: methyAnalysis is parent organization of: ARRmNormalization is parent organization of: ChIPsim is parent organization of: yaqcaffy is parent organization of: wateRmelon is parent organization of: sRAP is parent organization of: spotSegmentation is parent organization of: SNM is parent organization of: SNAGEE is parent organization of: Simpleaffy is parent organization of: qcmetrics is parent organization of: MANOR is parent organization of: limmaGUI is parent organization of: ffpe is parent organization of: dyebias is parent organization of: DEXUS is parent organization of: BeadDataPackR is parent organization of: aroma.light is parent organization of: ArrayTools is parent organization of: beadarray is parent organization of: arrayQuality is parent organization of: arrayMvout is parent organization of: affyQCReport is parent organization of: affyPLM is parent organization of: AffyExpress is parent organization of: waveTiling is parent organization of: gprege is parent organization of: oneChannelGUI is parent organization of: LMGene is parent organization of: factDesign is parent organization of: pickgene is parent organization of: betr is parent organization of: SCAN.UPC is parent organization of: arrayQualityMetrics is parent organization of: CALIB is parent organization of: DEDS is parent organization of: Harshlight is parent organization of: MiChip is parent organization of: OCplus is parent organization of: bridge is parent organization of: fRMA is parent organization of: genArise is parent organization of: lapmix is parent organization of: maCorrPlot is parent organization of: maSigPro is parent organization of: MACAT is parent organization of: maigesPack is parent organization of: MDQC is parent organization of: metaArray is parent organization of: nnNorm is parent organization of: plgem is parent organization of: PVCA is parent organization of: RAMA is parent organization of: stepNorm is parent organization of: virtualArray is parent organization of: LPE is parent organization of: vsn is parent organization of: ACME is parent organization of: CoGAPS is parent organization of: flowFP is parent organization of: rMAT is parent organization of: SLqPCR is parent organization of: nondetects is parent organization of: unifiedWMWqPCR is parent organization of: sSeq is parent organization of: CNVrd2 is parent organization of: plateCore is parent organization of: RSVSim is parent organization of: TCC is parent organization of: CQN is parent organization of: COMPASS is parent organization of: flowClust is parent organization of: SPADE is parent organization of: OrderedList is parent organization of: SamSPECTRAL is parent organization of: flowUtils is parent organization of: RchyOptimyx is parent organization of: TEQC is parent organization of: flowType is parent organization of: ADaCGH2 is parent organization of: flowViz is parent organization of: flowTrans is parent organization of: flowQB is parent organization of: shinyTANDEM is parent organization of: flowPlots is parent organization of: flowPhyto is parent organization of: flowCore is parent organization of: flowMerge is parent organization of: flowMap is parent organization of: flowMeans is parent organization of: spliceR is parent organization of: flowMatch is parent organization of: flowFit is parent organization of: flowCyBar is parent organization of: BEAT is parent organization of: flowBeads is parent organization of: CAMERA - Collection of annotation related methods for mass spectrometry data is parent organization of: MBASED is parent organization of: MethylAid is parent organization of: sapFinder is parent organization of: Pathview is parent organization of: DSS is parent organization of: RMassBank is parent organization of: iontree is parent organization of: Basic4Cseq is parent organization of: BiGGR is parent organization of: mzR is parent organization of: PAPi is parent organization of: CGHnormaliter is parent organization of: Chimera is parent organization of: BRAIN is parent organization of: tweeDEseq is parent organization of: SurvComp is parent organization of: Triplex is parent organization of: OmicCircos is parent organization of: ggbio is parent organization of: HTqPCR is parent organization of: NormqPCR is parent organization of: ddCt is parent organization of: EasyqpcR is parent organization of: SWAN is parent organization of: PING is parent organization of: DMRforPairs is parent organization of: SeqGSEA is parent organization of: h5vc is parent organization of: deepSNV is parent organization of: RUVSeq is parent organization of: BHC is parent organization of: epigenomix is parent organization of: IRanges is parent organization of: GeneNetworkBuilder is parent organization of: MethylSeekR is parent organization of: SRAdb is parent organization of: casper is parent organization of: htSeqTools is parent organization of: ChIPXpress is parent organization of: methVisual is parent organization of: DeconRNASeq is parent organization of: EDASeq is parent organization of: RIPSeeker is parent organization of: ShortRead is parent organization of: seqbias is parent organization of: DEGseq is parent organization of: arrayMagic is parent organization of: easyRNASeq is parent organization of: DNAcopy is parent organization of: CRLMM is parent organization of: motifRG is parent organization of: MMDiff is parent organization of: MiRaGE is parent organization of: LVSmiRNA is parent organization of: ExiMiR is parent organization of: RPA is parent organization of: CexoR is parent organization of: lumi is parent organization of: baySeq is parent organization of: tRanslatome is parent organization of: DNaseR is parent organization of: DEXSeq is parent organization of: ChIPpeakAnno is parent organization of: inSilicoMerging is parent organization of: minfi is parent organization of: Methylumi is parent organization of: miRNApath is parent organization of: sva package is parent organization of: dmrFinder is parent organization of: rqubic is parent organization of: BicARE is parent organization of: iBBiG is parent organization of: eisa is parent organization of: ChAMP is parent organization of: cghMCR is parent organization of: Bioconductor mailing list is parent organization of: DiffBind is parent organization of: NarrowPeaks is parent organization of: CSAR is parent organization of: CSSP is parent organization of: TargetScore is parent organization of: snapCGH is parent organization of: iChip is parent organization of: TurboNorm is parent organization of: Ringo is parent organization of: RLMM is parent organization of: charm is parent organization of: BiSeq is parent organization of: MEDME is parent organization of: MEDIPS is parent organization of: BayesPeak is parent organization of: ChIPseqR is parent organization of: Rolexa is parent organization of: cn.mops is parent organization of: RankProd is parent organization of: phyloseq is parent organization of: HiTC is parent organization of: CancerMutationAnalysis is parent organization of: aCGH is parent organization of: Repitools is parent organization of: flowPeaks is parent organization of: Mfuzz is parent organization of: les is parent organization of: OLIN is parent organization of: affylmGUI is parent organization of: CYCLE is parent organization of: r3Cseq is parent organization of: Piano is parent organization of: RamiGO hosts: DESeq hosts: rGADEM hosts: PICS hosts: Jmosaics hosts: R453Plus1Toolbox hosts: BAC hosts: targetscan.Hs.eg.db hosts: Starr hosts: Qvalue hosts: topGO hosts: MmPalateMiRNA hosts: CGHcall hosts: EGSEA hosts: NOISeq |
Catt Family Foundation ; Dana Farber Cancer Institute ; NHGRI R33 HG002708 |
PMID:15461798 | Free, Freely available | OMICS_01759, nif-0000-10445 | SCR_006442 | 2026-02-17 10:00:56 | 22974 | |||||||
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OpenBehavior Resource Report Resource Website 1+ mentions |
OpenBehavior (RRID:SCR_015938) | OB | software resource, software repository | Repository of open source tools for behavioral neuroscience research. OpenBehavior features hardware (tools, devices, apparatuses), as well as software for data acquisition and analysis and for the investigation of animal behavior and cognition. Dedicated to accelerating research through promotion of collaboration and open source projects. | software, data, hardware, animal, behavior, cognition, cognitive, analysis, processing |
lists: Feeding Experimentation Device project lists: Bpod lists: SLEAP, LEAP and MotionMapper project lists: Social LEAP lists: MotionMapper lists: Behavioral Segmentation of Open-field in DeepLabCut project lists: DeepBehavior project lists: BonZeb project lists: D-Track project lists: Online Animal Tracker project lists: Locomouse project lists: openEyeTrack project lists: DeepPoseKit project lists: DeepFly3D project lists: neurotic project lists: Rodent Arena Tracker project lists: Open Source Whisking Video Database portal lists: Simple Behavior Analysis project lists: OpenMonkeyStudio project lists: FaceSync project lists: Online Animal Tracker lists: DeepBehavior lists: BonZeb lists: Behavioral Segmentation of Open-field in DeepLabCut lists: FaceSync lists: LocoMouse lists: DeepPoseKit lists: openEyeTrack lists: D-Track lists: Simple Behavior Analysis lists: DeepFly3D lists: Open Source Whisking Video Database lists: neurotic lists: Low Cost Open Source Eye Tracking project lists: Stytra project lists: Calcium ActiVity Explorer project lists: idtracker.ai project lists: Live Mouse Tracker project lists: ToxTrac project lists: Picamera project lists: EthoScopes project lists: Worm Behavior Platform project lists: KineMouse Wheel project lists: Mousecam project lists: M-Track project lists: ezTrack project lists: FaceMap project lists: Head-Fixed Setup for Combined Behavior, Electrophysiology, and Optogenetics project lists: ZebraTrack project lists: LocoWhisk project lists: EthoWatcher project lists: Skinner Box project lists: Behavioral Observation Research Interactive Software project lists: Pyper project lists: Automated Rodent Tracker project lists: LinCoM project lists: Bonsai project lists: Quantifying Animal Movement from Pre-recorded Videos project lists: Platform for Acoustic STArtle project lists: Joystick project lists: 3DTracker project lists: AutoPilot project lists: PiDose project lists: DeepSqueak project lists: Rigbox project lists: Catalepsy Bar project lists: Dual port Lick Detector project lists: Pathfinder project lists: Actifield project lists: Rodent Activity Detector project lists: flyPAD project lists: Automated Home Cage Rodent Two bottle Choice Test project lists: MedParse project lists: Voluntary Access Static Incapacitance Chamber project lists: Laubach Lab GitHub Repository project lists: BPM Biosignals project lists: Automated mouse homecage two bottle choice test project lists: Mousetrap project lists: Autoreward2 project lists: Optimouse project lists: Hao Chen Lab Repository project lists: AutonoMouse project lists: Spike Forest project lists: Closed Loop System project lists: ArduiPod Box project lists: Oculomatic Eye Tracking project lists: Ultrasonic Vocalizations Detector project lists: Attys project lists: Calcium Imaging data Analysis project lists: Feldman Lab Lickometer project lists: MNE Scan project lists: Open Source platform for Sensory Tasks project lists: Scintillate project lists: Pypreclin project lists: Wave Surfer project lists: An open source motorized swivel for in vivo neural and behavioral recordings project lists: Toolboxes for Spike and LFP Analysis project lists: BrainGlobe project lists: UCLA Miniscope project lists: Cerebro Wireless Optogenetic System project lists: Home Cage Automated Skilled Reaching Apparatus project lists: Open-tES project lists: Capactive Touch Sensor project lists: CapTouch project lists: Two Armed Bandit Task project lists: Novel Gustometer for Human Taste Research project lists: OpenVape project lists: Calcium ActiVity Explorer lists: Pi Virtual Reality System project lists: BonVision project lists: FinchScope project lists: Mousecam lists: ezTrack lists: DIY-NAMIC project lists: Precision Syringe Pump Controller project lists: idtracker.ai lists: Stytra lists: EthoScopes lists: Worm Behavior Platform lists: Ardbark project lists: FaceMap lists: M-Track lists: ToxTrac lists: Pyper lists: Low Cost Open Source Eye Tracking lists: Automated Rodent Tracker lists: Live Mouse Tracker analysis lists: LinCoM lists: Skinner Box lists: 3DTracker lists: Pathfinder lists: Behavioral Observation Research Interactive Software lists: MNE Scan lists: Quantifying Animal Movement from Pre-recorded Videos lists: Rigbox lists: Platform for Acoustic STArtle lists: DeepSqueak lists: Oculomatic lists: Wave Surfer lists: EthoWatcher lists: MedParse lists: Bonsai lists: Scintillate lists: AutoPilot lists: Spike Forest lists: flyPAD lists: Optimouse lists: Calcium Imaging data Analysis lists: BonVision lists: Dual Port Lick Detector lists: Pypreclin lists: ACRoBaT lists: Visual stimulator with customizable light spectra lists: ToneBox lists: 3DOC lists: MouseBytes lists: Touchscreen Cognition lists: FreemoVR project lists: Modular Automated Platform for Large Scale Experiments project lists: OpenFeeder lists: SnackClock lists: SignalBuddy lists: ArControl project lists: Airtrack lists: Teensy-Based Interface project lists: Autonomous Training of a Forelimb Motor Task project lists: Ratcave project lists: DIY Rodent Running Disk lists: Moving Wall Box lists: Operant Box for Auditory Tasks project lists: Camera Control project lists: FlyPi lists: CerebraLux lists: Automated Home-Cage Functional Imaging project lists: Pearce Lab Syringe Pump project lists: Craniobot project lists: PhotometryBox lists: Pulse Pal project lists: NINscope lists: Nose Poke Device lists: pyControl project lists: OpenMV project lists: Rodent Operant Bucket project lists: Tetroplater lists: OpenSpritzer lists: Argus lists: NeRD lists: PRiED lists: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project lists: MouseMove project lists: Eco-HAB lists: Homecage Task Training and Mesoscale Imaging project lists: Microwave based Homecage Motion Detector project lists: CHEndoscope lists: Robotic Flower System for Bee Behavior project lists: TRIO Platform lists: A Head Mounted Multi Camera System for Freely Moving Mice project lists: Ratcave lists: 4 Port Nose Poke lists: An Opensource lickometer and microstructure analysis program lists: Automated Classification of Self-grooming in Mice project lists: FreemoVR lists: ArControl lists: Visual Discrimination with an iPad lists: Teensy-Based Interface lists: Operant Box for Auditory Tasks lists: Autonomous Training of a Forelimb Motor Task lists: 3D Printed Headcap and Microdrive lists: poke device arduino lists: MouseBytes lists: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology lists: Rodent Operant Bucket lists: Camera Control lists: linear actuator lists: Modular Automated Platform for Large Scale Experiments lists: pyControl lists: Argus lists: NINscope software lists: OpenMV lists: MouseMove lists: chendoscope lists: craniobot lists: Pulse Pal lists: Automated Home-Cage Functional Imaging lists: AutoHeadFix lists: SpikeGadgets lists: Open Ephys lists: MRI-stereoscope project lists: AutomaticSleepScoringTool lists: Pi-based Remote Acquisition Technology for Motion Capture project lists: Pi-based Remote Acquisition Technology for Motion Capture lists: Brainrender lists: TetrODrive lists: COMPASS lists: Cellpose lists: OORTT lists: DBscorer lists: GazeMetrics lists: AutoStereota lists: FlyBrainLab lists: pyOS-5 project lists: Pyneal lists: pyOS-5 lists: Atlas Based Analysis lists: VocalMat lists: DABEST lists: Raspberry Pi based auditory stimulus generator lists: Pain Assessment at Withdrawal Speeds lists: Florida research open source synchronization tool lists: Permuco lists: LED Matrix Stimuli lists: Mouse Action Recognition System lists: Behavior Ensemble and Neural Trajectory Observatory lists: Neonatal Stereotaxic Mouse Adaptor lists: MARS Developer lists: EZcalcium lists: MRI Compatible Microdrive lists: GuPPy lists: DeepEthogram lists: Pycro Manager lists: DeepBhvTracking lists: TweetyNet lists: OpenPose lists: TRex lists: SIPEC lists: Closed Loop Automated Reaching Apparatus lists: Timed pressure control hardware and software for delivery of air mediated distensions in animal models lists: CellExplorer lists: DLStream lists: SipperViz lists: Variational Embedding of Animal Motion lists: SHARCQ lists: PavCA project lists: GoFish Ajuwon etal 2022 lists: LED Zappelin’ lists: Minian lists: Modular LED Displays project lists: OpenSync lists: USVCAM lists: Histological E data Registration in rodent Brain Spaces lists: Pi USB Cam project lists: 3D Printed Superfusion Chamber lists: pyPhotometry lists: Rtrack lists: ColonyTrack lists: Anipose lists: LiftPose3D lists: DANNCE lists: DeepLabCut Project lists: ACTman lists: Raspberry Pi Grating lists: Falcon lists: OpBox lists: Mouse Behavioral Analysis Toolbox lists: Pynapple lists: Wheel Running Activity acQuisition lists: CaT-z lists: M3 Platform lists: Automated 2 Photon Imaging Compatible Platform for Assessing Working Memory lists: Rasberry rat lists: RodentJoystick lists: tmilltracker lists: 3D Printed Multi Pump System lists: BehaviorDEPOT lists: Open Face Homecage Running Wheel lists: RatHeadphones lists: RatInABox lists: LabNet lists: JAX Animal Behavior System lists: AnimalTA lists: Mousebytes lists: Lick Instance Quantifier Home cage Device lists: B-CALM lists: Freibox lists: commutator lists: Customized Guide Cannulas lists: BrainWAVE lists: Brainways lists: LFP Monitoring lists: PyMouseTracks lists: Lightning Pose lists: Customizable Multielectrode Array lists: Live Mouse Tracker Toolkit Analysis lists: HFOApp lists: Synaptic Vesicles Detection lists: Pipette Finding CNN lists: 3DP Gustometer lists: SEB3R lists: Lickometer Box lists: Custom-fitting-of-implants lists: Markerless Mouse Tracking for Social Experiments lists: FARESHARE lists: HERBs lists: E-Scope lists: PyBehave lists: ReachOut lists: One-rat Turnstile lists: TD_Drive lists: Holeboard lists: SaLSa lists: ghostipy lists: DREAM implant lists: HSSM lists: High-Precision Optical Fiber-Based Lickometer lists: NC4gate lists: ArUco lists: STPoseNet lists: Bell Jar lists: Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats |
Public | SCR_015938 | 2026-02-17 10:02:37 | 4 | |||||||||
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Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators. | stem cell, facility, la jolla, pluripotent stem cells, ipsc, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014856 | SBP Medical Discovery Institute Stem Cell Core, SBP Stem Cell Core | 2026-02-17 10:02:45 | 0 | ||||||||||
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Montana State University Bioinformatics Core Facility Resource Report Resource Website |
Montana State University Bioinformatics Core Facility (RRID:SCR_009937) | core facility, access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research. | nucleic, acid, microarray, assay, database, development, analysis, genome, assembly, pathway, data, gene, expression, metagenomics |
is listed by: Eagle I has parent organization: Montana State University |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156405 | http://cores.montana.edu/bioinformatics/ | SCR_009937 | , Montana State University, core facility, MSU, Bioinformatics Core Laboratory | 2026-02-17 10:01:32 | 0 | |||||||
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Georgia Genomics and Bioinformatics Core at the University of Georgia Resource Report Resource Website 50+ mentions |
Georgia Genomics and Bioinformatics Core at the University of Georgia (RRID:SCR_010994) | GGBC | training service resource, service resource, access service resource, core facility | Core laboratory for nucleic acid sequencing and bioinformatics. Used for research support, education, and training. Services include genomic techniques and applications, sequencing technologies, and bioinformatics analyses, writting letters of support for grant applications submitted to funding agencies. GGBC operates multiple platforms for short-, long-, and single-molecule sequencing reads (i.e., Illumina MiSeq and NextSeq, PacBio Sequel, and Oxford Nanopore MinIon). | nucleic, acid, sequencing, labs, analysis, equipment, genomic, technique, analysis, grant, application |
is listed by: ScienceExchange is related to: University of Georgia Labs and Facilities has parent organization: University of Georgia; Georgia; USA |
SciEx_9234 | http://www.scienceexchange.com/facilities/georgia-genomics-facility-uga, http://www.scienceexchange.com/facilities/georgia-genomics-facility-uga | SCR_010994 | Georgia Genomics & Bioinformatics Core, Georgia Genomics and Bioinformatics Core at UGA, University of Georgia Genomics Facility, Georgia Genomics and Bioinformatics Core | 2026-02-17 10:01:54 | 71 | |||||||
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University of Salerno Laboratory of Molecular Medicine and Genomics Resource Report Resource Website |
University of Salerno Laboratory of Molecular Medicine and Genomics (RRID:SCR_011047) | UNISA LMMGe, UNISA, LMMGe, UNISA Laboratory of Molecular Medicine and Genomics, Laboratory of Molecular Medicine and Genomics | service resource, access service resource, core facility | Core equipped for structural and functional studies of genomes, includes equipment for next generation sequencing applications (Illumina HiSeq 1500, GAIIx and MiSeq, Life Technologies Ion Torrent PGM), RNA and microRNA expression profiling, array-based DNA methylation analyses and SNP genotyping (Illumina HiScan and Agilent High Resolution microarray scanners), informatics and bioinformatics (a server farm for genomics data computation and a high capacity data storage unit), fluorescence and confocal microscopy, long-term sample storage, cell culture, including a facility for generation and handling of viral vectors for gene transfer and gene therapy, access to a small animal facility for ''in vivo'' experimentations. Trained biotechnologists, molecular biologists and bioinformaticians handle all aspects related to experimental design, technical implementation and data analysis and storage. | genomes, sequencing, implementation, analysis, genotyping, cell culture, |
is listed by: ScienceExchange has parent organization: University of Salerno; Salerno; Italy |
Available to external user | SciEx_9722 | http://www.scienceexchange.com/facilities/laboratory-of-molecular-medicine-and-genomics | SCR_011047 | Laboratory of Molecular Medicine and Genomics, University of Salerno, UNISA, LMMGe | 2026-02-17 10:01:55 | 0 | ||||||
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University of Southern California School of Pharmacy Translational Research Laboratory Resource Report Resource Website |
University of Southern California School of Pharmacy Translational Research Laboratory (RRID:SCR_012253) | USC, School of Pharmacy, TRLab, Translational Research Lab, University of Southern California, School of Pharmacy | service resource, access service resource, core facility | Core is equipped with a wide variety of technologically advanced instruments essential for cutting edge biomedical discovery and therapeutic development research. TRLab is composed of two major units. The Computational Bioinformatics Unit houses graphic workstations and modeling programs that enable in silico virtual screening and rational drug design applications. The Therapeutic Screening Unit houses a number of specialized instruments that enable a broad range of automated and multiplexed biological analyses in a throughput manner. The core mission of the TRLab has been to provide investigators with a state-of-the-art technological platform and technical expertise to advance translational research endeavors in the School of Pharmacy and at USC. | immunobiology, Molecular biology, analysis, imaging, |
is listed by: ScienceExchange has parent organization: University of Southern California; Los Angeles; USA |
Available to external user | SciEx_11044 | http://www.scienceexchange.com/facilities/the-translational-research-laboratory | SCR_012253 | USC, Translational Research Lab, Translational Research Laboratory, TRLab, University of Southern California, School of Pharmacy | 2026-02-17 10:02:10 | 0 | ||||||
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Hunter NMR Spectroscopy Facility Resource Report Resource Website |
Hunter NMR Spectroscopy Facility (RRID:SCR_000883) | material resource, instrument supplier | A service facility with four main spectrometers. The facility consists of four NMR instruments: a JEOL GX-400, a Varian Inova 500, a Bruker Avance 500 equipped with a 13C-1H cryoprobe, and a Bruker Avance III 600 MHz spectrometer equipped with a cryoprobe. These spectrometers are utilized by scientists from Hunter College, as well as from the entire CUNY community. The large variety of available probes allows detection of virtually any MR-active nuclide. Data analysis is performed either at the spectrometer workstation with vendor software or off-line with third party software packages. | spectrometer, spectroscopy, analysis, cuny, nuclide, data analysis |
is listed by: Eagle I has parent organization: Hunter College; New York; USA |
nlx_156342 | http://hunter-cuny.eagle-i.net/i/00000136-79a2-306f-949b-425080000000 | SCR_000883 | 2026-02-17 09:59:33 | 0 | |||||||||
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National Magnetic Resonance Facility at Madison Resource Report Resource Website 1+ mentions |
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) | NMRFAM | training resource, service resource, access service resource | Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols. | nmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology center | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIGMS R24GM141526; NIGMS P41136463 |
Free, Freely Available | nlx_152672 | SCR_001449 | 2026-02-17 09:59:37 | 4 |
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