Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SPARC Portal Resource Report Resource Website 100+ mentions |
SPARC Portal (RRID:SCR_017041) | SPARC.science | data repository, service resource, storage service resource | SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short. | Nervous system, periphery, organ, human, FASEB list, repository, curated |
uses: Protocols.io uses: Brain Imaging Data Structure (BIDs) uses: Physiome Model Repository uses: SciGraph uses: o²S²PARC uses: SODA uses: Blackfynn Discover uses: ApiNATOMY uses: Biolucida uses: TissueMaker uses: ScaffoldMaker uses: ScaffoldFitter uses: OpenCOR uses: Pennsieve Data Management Platform uses: InterLex uses: Neurolucida 360 uses: SciCrunch uses: Tissue Mapper uses: Vesselucida 360 uses: DataCite uses: TissueMaker is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is recommended by: National Library of Medicine is related to: SPARC Anatomy Working Group is related to: HORNET CENTER FOR AUTONOMIC NERVE RECORDING AND STIMULATION SYSTEMS is related to: NIH PRECISION Human Pain Network is related to: SCKAN Explorer is related to: SCKANNER works with: SPARC Data Standard has organization facet: o²S²PARC has organization facet: SODA has organization facet: SPARC Anatomy Working Group has organization facet: Blackfynn Discover has organization facet: ApiNATOMY has organization facet: Pennsieve Data Management Platform |
OD OD023849; OD OD024908; OD OD025306; OD OD025349; OD OD026585; OD OD030213; OD OD030541; OD OD032619 |
PMID:34248680 DOI:10.1101/2021.02.10.430563 |
Free, Freely available, | DOI:10.26275, r3d100013719 | https://commonfund.nih.gov/sparc, https://docs.sparc.science/, https://data.sparc.science/, https://doi.org/10.26275, https://doi.dx/10.26275, https://sparc.science/data?type=dataset, https://doi.org/10.17616/R31NJN2V | SCR_017041 | SciCrunch Registry | , SPARC Project, SPARC Repository, Stimulating Peripheral Activity to Relieve Conditions | 2026-11-07 11:58:27 | 119 | ||||
|
nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | JDRF ; NCI R33 CA225248; NIBIB R21 EB020976; NIDDK DP3 DK110844; NIDDK UC4 DK104167; NIGMS P41 GM103493; OD S10 OD016350 |
PMID:29491378 | SCR_017129 | SciCrunch Registry | 2026-11-07 11:58:45 | 1 | |||||||||
|
Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | data analysis software, data processing software, software application, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | Cancer Prevention Research Institute of Texas ; Google Research Award ; IBM University Challenge Award ; McNair Medical Institute Scholar Award ; NHGRI HG003067; NHGRI HG006193; NHLBI U01 HL130010; NSF PHY-1427654; NVIDIA Research Center Award ; OD DP2 OD008540; PD Soros Fellowship ; President Early Career Award in Science and Engineering ; Welch Foundation |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | SciCrunch Registry | 2026-11-07 11:58:46 | 119 | ||||||||
|
Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; OD OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | SciCrunch Registry | 2026-11-07 11:58:52 | 6 | ||||||
|
Wisconsin National Primate Research Center Resource Report Resource Website 1+ mentions |
Wisconsin National Primate Research Center (RRID:SCR_012987) | WNPRC | data or information resource, portal, service resource, topical portal | Research center aimed towards increasing understanding of basic primate biology and improving human health and quality of life. Its goals include helping discover treatments, preventative measures and cures for human disease; gathering knowledge of primate biology and ecosystems; providing resources to scientists world wide; and collecting and disseminating research to the larger scientific community and public. | NPRC, NPRC Consortium, ORIP, ecosystem, embryonic, fertility, fetal, gene, animal, ctl, development, differentiation, disease, hiv, immunodeficiency, immunogenetic, medicine, metabolic, molecular, neuroendocrinology, obesity, ocular, ovarian, parkinson's disease, polycystic, presbyopia, primate, reproduction, restriction, stem cell, t-cell, vaccine, virology, virus, caloric restriction, obesity, diabetes mellitus, osteoporosis, ocular aging, glaucoma, neurodegeneration, gene expression profiling, simian immunodeficiency virus, cytotoxic t cell, embryonic stem cell, fertility regulation, embryonic differentiation, maternal-fetal health, reproductive neuroendocrinology, polycystic ovarian syndrome, endometriosis, reproductive tract, gene therapy |
is listed by: Biositemaps is listed by: National Primate Research Center Consortium is related to: NIA Nonhuman Primate Tissue Bank has parent organization: University of Wisconsin-Madison; Wisconsin; USA is parent organization of: Primate Info Net is parent organization of: Wisconsin National Primate Research Center Pathology Services Core Facility |
Aging | NCRR RR000167; OD P51 OD011106 |
Available to the research community | nif-0000-24362 | https://orip.nih.gov/comparative-medicine/programs/vertebrate-models | SCR_012987 | SciCrunch Registry | 2026-11-07 11:57:41 | 3 | |||||
|
neurodata Resource Report Resource Website 50+ mentions |
neurodata (RRID:SCR_014264) | data or information resource, data repository, image repository, portal, project portal, service resource, software resource, storage service resource | Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs. | neuroscience, neuroimage, graph explorer, data repository, johns hopkins university, BRAIN Initiative, FASEB list |
is related to: Open Connectome Project has parent organization: Johns Hopkins University; Maryland; USA |
DARPA ; NIBIB R01 EB016411; NIDA R01 DA036400; NSF 1707298; NSF ACI-1261715; NSF OCI-1040114; OD R01 OD19123 |
Free, Freely available | https://neurodata.io/tools/ | SCR_014264 | SciCrunch Registry | 2026-11-07 11:57:58 | 94 | ||||||||
|
CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | data access protocol, service resource, software resource, web service | Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design. | Design tool, CRISPR mediated gene editing, gene repression, gene activation, guide RNA design, genome, automated genome, sgRNA design, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
FANEDD ; NIDA R01 DA036858; NIDCR ; NSFC ; OD ; OD OD017887 |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | SciCrunch Registry | CRISP-Editing, Repression and Activation | 2026-11-07 11:58:55 | 13 | |||||
|
microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, software resource, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | Austrian Science Fund ; German Research Foundation ; Korean Government ; Mexican National Council of Science and Technology ; NIAID R01AI167860; NIA U19AG063744; NIDDK T32DK007202; NIDDK U01DK119702; NIDDK U24DK133658; NIGMS 1DP2GM137413; NIGMS 1R01GM132649; NIGMS R01GM107550; NIGMS R35GM142938; NLM 1R01LM013115; NSF ; OD S10 OD021750; Research Council of Norway ; Sao Paulo Research Foundation |
PMID:37577622 | Free, Freely available, | SCR_024713 | SciCrunch Registry | 2026-11-07 12:01:19 | 7 | ||||||||
|
Drosophila Genomics Resource Center Resource Report Resource Website 500+ mentions |
Drosophila Genomics Resource Center (RRID:SCR_002845) | DGRC | biomaterial supply resource, cell repository, material resource | Serves Drosophila research community by collecting and distributing DNA clones and vectors; collecting and distributing Drosophila cell lines; developing and testing genomics technologies for use in Drosophila and assisting members of the research community in their use. | RIN, Resource Information Network, expression, gene, array, cell, clone, dna, drosophila, genomics, karyotype, material, microarray, reagent, research, technology, transcriptome, transformation, vector, FASEB list, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network has parent organization: Indiana University; Indiana; USA works with: Cellosaurus |
OD P40 OD010949 | Restricted | nif-0000-25420 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | https://dgrc.cgb.indiana.edu/ | SCR_002845 | SciCrunch Registry | Drosophila Genomics Resource Center at Indiana University | 2026-11-07 12:01:24 | 618 | ||||
|
Drosophila RNAi Screening Center Resource Report Resource Website 1+ mentions |
Drosophila RNAi Screening Center (RRID:SCR_000733) | DRSC | data or information resource, database | Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays. | genome, screening, drosophila, fly, insect, rnai | has parent organization: Harvard University; Cambridge; United States | OD R24 OD011176 | PMID:16381918 | nif-0000-02846 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, http://flyRNAi.org/cgi-bin/RNAi_screens.pl | SCR_000733 | SciCrunch Registry | Development of Validated Drosophila in vivo RNAi Models of Human Diseases | 2026-11-07 12:02:15 | 2 | |||||
|
Baylor College of Medicine Human Genome Sequencing Center Resource Report Resource Website 50+ mentions |
Baylor College of Medicine Human Genome Sequencing Center (RRID:SCR_013605) | BCM-HGSC | analysis service resource, production service resource, service resource | Center for high-throughput DNA sequence generation and the accompanying analysis. The sequence data generated by the center's machines are analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI). | next-generation sequencing, genetic variation, genome, dna sequence, FASEB list |
has parent organization: Baylor University; Texas; USA is parent organization of: Mercury is parent organization of: xAtlas |
OD R24 OD011173 | nif-0000-10162 | SCR_013605 | SciCrunch Registry | Human Genome Sequencing Center, BCM HGSC | 2026-11-07 12:03:13 | 65 | |||||||
|
Microphysiology Systems Database Resource Report Resource Website 1+ mentions |
Microphysiology Systems Database (RRID:SCR_021126) | MPS-Db | data or information resource, database | Open source database used for analyzing and modeling compound interactions with human and animal organ models.Platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. Resource for relating in vitro organ model data to multiple biochemical, preclinical, and clinical data sources on in vivo drug effects. | Compound interactions, human organ models, animal organ models, analyzing interactions, modeling interactions, |
is used by: NIH Heal Project is listed by: re3data.org |
NCATS UH3 TR00503; OD S10 OD01226; U.S. Environmental Protection Agency |
PMID:28781990 | Free, Freely available | SCR_021126 | SciCrunch Registry | MPS database | 2026-11-07 12:03:22 | 4 | ||||||
|
National Swine Resource and Research Center Resource Report Resource Website 50+ mentions |
National Swine Resource and Research Center (RRID:SCR_006855) | NSRRC | biomaterial supply resource, cell repository, material resource, organism supplier | Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. | RIN, Resource Information Network, pig, fetal fibroblast, live animal, tissue, fibroblast, fetus, genetically modified pig, biomaterial manufacture, genome, genotyping, genetics, reproduction, breeding, health monitoring, cryopreservation, phenotyping, consulting, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NHLBI ; NIAID ; OD U42 OD011140 |
Public, To investigators, Application required | nif-0000-12086 | SCR_006855 | SciCrunch Registry | National Swine Resource Research Center | 2026-11-07 12:00:37 | 79 | ||||||
|
Fitness Browser Resource Report Resource Website 1+ mentions |
Fitness Browser (RRID:SCR_018981) | data access protocol, data or information resource, software resource, web service | Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function. | Genome browser, bacteria, mutant phenotype, bacterial genes, unknown function, data | has parent organization: University of California at Berkeley; Berkeley; USA | NCRR S10 RR027303; NCRR S10 RR029668; OD OD018174; Office of Science of the US Department of Energy |
PMID:29769716 | Free, Freely available | SCR_018981 | SciCrunch Registry | 2026-11-07 12:00:51 | 9 | ||||||||
|
nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | data processing software, image processing software, software application, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; Multidisciplinary University Research Initiative Army Research Office ; NIAID R01AI130303; NIGMS F31GM116517; NIGMS P41GM10371; NIMH P50MH09427; NIMH R01MH110932; NINDS R01NS076467; NINDS R01NS095367; NINDS U01NS090449; NSF NSF-1707316; OD DP2OD006514 |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | SciCrunch Registry | 2026-11-07 12:01:07 | 0 | ||||||||
|
ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | software resource, web application | Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries. | Transcription Factor, gene sets, transcription factor enrichment analysis, TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, TF-gene co-occurrence, prediction of correct upstream, | NCI U24CA224260; NHLBI U54HL127624; NIGMS T32GM062754; OD OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | SciCrunch Registry | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-11-07 12:01:04 | 193 | |||||||
|
Kinase Enrichment Analysis 3 Resource Report Resource Website 10+ mentions |
Kinase Enrichment Analysis 3 (RRID:SCR_023623) | KEA3 | data access protocol, software resource, web service | Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations. | overrepresentation of upstream kinases, upstream kinases, upstream kinases substrates, user inputted list of proteins, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; OD OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | SciCrunch Registry | 2026-11-07 12:01:12 | 16 | |||||||
|
GeneRanger Resource Report Resource Website |
GeneRanger (RRID:SCR_023622) | data access protocol, software resource, web service | Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types. | explore single gene expression, gene expression across tissues and cell types, gene expression, |
is related to: TargetRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA224260; NCI U24CA264250; NCI U24CA271114; NIDDK R01DK131525; NIDDK RC2DK131995; OD OT2OD030160 |
PMID:37166966 | Free, Freely available | SCR_023622 | SciCrunch Registry | 2026-11-07 12:01:08 | 0 | ||||||||
|
TargetRanger Resource Report Resource Website 1+ mentions |
TargetRanger (RRID:SCR_023621) | data access protocol, software resource, web service | Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines. | identify targets, identify genes, user inputted RNA-seq samples, target cells, proteomics data, human cells, |
is related to: GeneRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA224260; NCI U24CA264250; NCI U24CA271114; NIDDK R01DK131525; NIDDK RC2DK131995; OD OT2OD030160 |
PMID:37166966 | Free, Freely available | https://maayanlab.github.io/Workshop.io/generanger | SCR_023621 | SciCrunch Registry | 2026-11-07 12:01:04 | 2 | |||||||
|
Patient-Reported Outcomes Measurement Information System Resource Report Resource Website 1000+ mentions |
Patient-Reported Outcomes Measurement Information System (RRID:SCR_004718) | PROMIS | assessment test provider, material resource | Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children. | adult, child, assessment, clinical, anger, pain, fatigue, physical function, depression, anxiety, social function, patient reported outcome, health, measure |
is recommended by: National Library of Medicine has parent organization: University of Washington; Seattle; USA |
NCCIH ; NCI ; NHLBI ; NIAMS ; NIA ; NIDA ; NIDCD ; NIDDK ; NIMH ; NINDS ; NINR ; OD |
nlx_143881 | http://www.healthmeasures.net/index.php?option=com_content&view=category&layout=blog&id=71&Itemid=817 | SCR_004718 | SciCrunch Registry | PROMIS, Patient Reported Outcomes Measurement Information System | 2026-11-07 12:03:34 | 3303 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
