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 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CalR Resource Report Resource Website 100+ mentions |
CalR (RRID:SCR_015849) | data analysis software, data processing software, data visualization software, software application, software resource, web application | A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates. | indirect, calorimerty, analysis, visualization, energy, balance, food intake, energy expenditure, metabolism, metabolic phenotyping, CLAMS, PhenoMaster, Prometheon, biostatistics, ANCOVA, reproducibility, Columbus Instruments, Sable Systems, TSE | is related to: Harvard University; Cambridge; United States | Harvard Digestive Disease Center ; Mouse Metabolic Phenotyping Center ; NIDDK |
DOI:10.1101/213967 | Freely available, Public | https://calrapp.org | SCR_015849 | SciCrunch Registry | A Web Application for Indirect Calorimetry Analysis | 2026-10-24 12:47:29 | 228 | ||||||
|
Pediatric Obesity Microbiome and Metabolism Study Resource Report Resource Website 1+ mentions |
Pediatric Obesity Microbiome and Metabolism Study (RRID:SCR_021071) | POMMS | biospecimen repository, data or information resource, disease-related portal, material storage repository, portal, service resource, storage service resource, topical portal | Biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.Biorepository is available as shared resource. | Gut microbiome analysis, marker gene, shotgun DNA sequencing, clinical data, metabolomic data, microbiome samples, biorespository, adolescent obesity |
has parent organization: Duke University; North Carolina; USA has parent organization: Northwestern University; Illinois; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Obesity | NIDDK R24 DK110492 | DOI:10.1002/oby.23081 | Free, Freely available | SCR_021071 | SciCrunch Registry | 2026-10-24 12:48:49 | 1 | ||||||
|
CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI R00 HG008399; NHGRI R01 HG005085; NHGRI RM1 HG009490; NHLBI P01 HL32262; NHLBI R01 HL119099; NIBIB R01 EB022376; NIDDK P30 DK049216; NIDDK R03 DK109232; NIGMS R35 GM118062; NIGMS R35 GM118158 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2, https://github.com/pinellolab/CRISPResso | SCR_021538 | SciCrunch Registry | CRISPResso2 | 2026-10-24 12:48:55 | 27 | |||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | SciCrunch Registry | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-10-24 12:47:03 | 1418 | ||||
|
Metabolomics Workbench Resource Report Resource Website 500+ mentions |
Metabolomics Workbench (RRID:SCR_013794) | MetWB | data or information resource, data repository, service resource, storage service resource | Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops. | repository, metabolomics, database, funding, training, protocol, bio.tools, FASEB list, DRKB |
is used by: NIH Heal Project 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 lists: NIH Metabolomics program lists: MetaCore lists: JMP lists: STATISTICA lists: Spotfire lists: Coordination of Standards in Metabolomics lists: MetaboLights lists: MetabolomeXchange lists: Metabolomics Society lists: Birmingham Metabolite Library lists: Glycan Mass Spectral Database (GMDB) lists: Mass Spectral Library lists: mzCloud lists: MetabolomeExpress lists: Spectral Database System (SDBS) lists: CTSgetR lists: Hierarchical Clustering lists: imDEV lists: Linear Discriminant Analysis lists: Principal Components Analysis lists: mwtabR lists: 3Omics lists: ACD/ NMR Processor lists: NIST Mass Spectrometry Data Center lists: Chemical Translation Service lists: Chenomx NMR Suite lists: DeviumWeb lists: MBRole lists: MetaMapR lists: MetaP lists: Metscape lists: SIMCA lists: TeachingDemos is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is listed by: re3data.org is listed by: DataCite has parent organization: University of California; California; USA is parent organization of: Metabolomics Workbench Metabolite Database |
NIDDK DK141185; NIH |
Free, Freely available | biotools:Metabolomics_Workbench, r3d100012314 | https://bio.tools/Metabolomics_Workbench, https://api.datacite.org/dois?prefix=10.21228 | SCR_013794 | SciCrunch Registry | Metabolomics Workbench, MetWB, UCSD Metabolomics Workbench, Metabolomics Workbench (MetWB) | 2026-10-24 12:47:10 | 666 | |||||
|
Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data analysis software, data processing software, software application, software resource | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NCRR P41 RR011823; NHLBI R01 HL082747; NIA P30 AG013280; NIDDK R01 DK069386 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | SciCrunch Registry | 2026-10-24 12:47:12 | 3040 | ||||||||
|
HIRN Consortium on Modeling Autoimmune Interactions Resource Report Resource Website 1+ mentions |
HIRN Consortium on Modeling Autoimmune Interactions (RRID:SCR_016200) | HIRN-CMAI | consortium, data or information resource, organization portal, portal | Consortium that is an independent research initiative of the Human Research Information Network (HIRN). It is developing innovative approaches to model basic aspects of human T1D immunobiology using novel in vivo and in vitro platforms. | autoimmune, disease, immunobiology, in vitro, research, in vivo | is organization facet of: Human Islet Research Network (HIRN) | NIDDK ; NIDDK U01 DK104162; NIDDK U01 DK107383; NIDDK UC4 DK104194; NIDDK UC4 DK104207; NIDDK UC4 DK104218; NIDDK UC4 DK104223; NIDDK UC4 DK116284 |
SCR_016200 | SciCrunch Registry | Consortium on Modeling Autoimmune Interactions (HIRN-CMAI) | 2026-10-24 12:47:33 | 1 | ||||||||
|
HIRN Bioinformatics Center Resource Report Resource Website 1+ mentions |
HIRN Bioinformatics Center (RRID:SCR_016203) | HIRN-BC | consortium, data or information resource, organization portal, portal | The Bioinformatics Center is located within the Department of Diabetes and Cancer Discovery Science at City of Hope and was established in 2014 to support the Human Islet Research Network (HIRN). The overall objective of the Bioinformatics Center is to advance type 1 diabetes knowledge generated through HIRN by providing the bioinformatics capability and infrastructure needed to support the Network. To achieve this goal, the Bioinformatics Center provides investigators with tools, processes, and methods to facilitate long term sharing, maintenance, and management of HIRN developed resources, including datasets, technologies, documents, and bioreagents. Collaboration and communication are cultivated through consultation and outreach activities. In 2019, HIRN received funding to continue HIRN Coordinating Center (CC) and Bioinformatics Center (BC) as Human Islet Research Enhancement Center (HIREC). | bioinformatics, sharing, maintenance, data set, bioengineering | is organization facet of: Human Islet Research Network (HIRN) | Type 1 diabetes, Diabetes | NIDDK ; NIDDK U01 DK104147 |
http://bclabs.hirnetwork.org/ | SCR_016203 | SciCrunch Registry | 2026-10-24 12:47:33 | 1 | |||||||
|
Diabetes Epigenome Atlas Resource Report Resource Website 1+ mentions |
Diabetes Epigenome Atlas (RRID:SCR_016441) | atlas, data or information resource, database, disease-related portal, portal, topical portal | Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers. | collect, provide, data, human, genome, epigenome, genetic, study, type 2 diabetes |
has parent organization: Stanford University; Stanford; California has parent organization: University of California at San Diego; California; USA |
type 2 diabetes | NIDDK U01 DK100554 | Free, Proprietary data are available only to approved AMP consortium users with user accounts | SCR_016537 | SCR_016441 | SciCrunch Registry | 2026-10-24 12:47:39 | 2 | |||||||
|
biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | data analysis software, data processing software, software application, software resource, software toolkit | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
ARO W911NF1110473; NHGRI R01 HG005220; NHGRI R01 HG005969; NIDDK U54 DE023798; NSF DBI1053486; Sloan Foundation 4406J0B |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery, https://bio.tools/biobakery | SCR_016596 | SciCrunch Registry | bioBakery, biobakery | 2026-10-24 12:47:38 | 18 | |||||
|
PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | data analysis software, data processing software, software application, software resource | Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype. | detect, gene, disease, associate, trait, mechanism, molecular, variation, phenotype | NCI F32CA165823; NCI K12 CA139160; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595; NIGMS U01 GM092691; NIGMS U01 GM61393; NIMH P50 MH094267; NIMH R01 MH090937; NIMH R01 MH101820; NIMH T32 MH020065 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | SciCrunch Registry | 2026-10-24 12:47:40 | 25 | |||||||||
|
sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | data analysis software, data processing software, software application, software resource | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NHGRI R01 HG006129; NIDDK R01 DK094699 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth, https://bio.tools/sleuth, https://bio.tools/sleuth | SCR_016883 | SciCrunch Registry | 2026-10-24 12:47:41 | 28 | ||||||
|
ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 10+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | catalog, data or information resource, database, portal, project portal | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIDDK ; NIH |
SCR_016921 | SciCrunch Registry | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-10-24 12:47:41 | 11 | ||||||||
|
PyMINEr Resource Report Resource Website 1+ mentions |
PyMINEr (RRID:SCR_016990) | data analysis software, data processing software, software application, software resource | Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. | automate, cell, type, identification, pathway, analysis, gene, regulation, autocrine, paracrine, signaling, network, human, islet, scRNA-seq, dataset | Carver Chair in Molecular Medicine ; Fraternal Order of Eagles Diabetes Research Center ; NHLBI R24 HL123482; NIDDK R01 DK115791; NIDDK R24 DK096518; NIGMS T32 GM082729; University of Iowa Center for Gene Therapy |
PMID:30759402 | Free, Available for download, Freely available, Tutorial available | SCR_016990 | SciCrunch Registry | 2026-10-24 12:47:42 | 5 | |||||||||
|
SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SciCrunch Registry | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-10-24 12:50:33 | 740 | |||||
|
GATACA GUDMAP Gene Explorer Resource Report Resource Website |
GATACA GUDMAP Gene Explorer (RRID:SCR_014518) | data or information resource, database | A database which can be used to search for genes critical for a variety of Genito-Urinary system functions and diseases. | genito-urinary system, genes, genetic diseases |
uses: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) has parent organization: GenitoUrinary Development Molecular Anatomy Project |
NIDDK | Freely available | SCR_014518 | SciCrunch Registry | 2026-10-24 12:51:11 | 0 | |||||||||
|
HIRN Human Pancreas Analysis Program Resource Report Resource Website 100+ mentions |
HIRN Human Pancreas Analysis Program (RRID:SCR_016202) | HIRN-HPAP, HPAP | data or information resource, database | Program is performing deep phenotyping of human endocrine pancreas and its interaction with immune system to better understand cellular and molecular events that precede and lead to beta cell loss in Type-1 Diabetes (T1D) and islet dysfunction in Type-2 Diabetes (T2D). | pancreas, endocrinology, immunology, molecular, biology, human, t1d, beta cell, RIN, RRID Community Authority, |
has parent organization: HIRN Human Pancreas Analysis Consortium is organization facet of: Human Islet Research Network (HIRN) |
Type 1 diabetes, Diabetes | NIDDK ; NIDDK U01 DK104162; NIDDK UC4 DK112217; NIDDK UC4 DK112232 |
PMID:31127054 | https://hirnetwork.org/consortium/hpap | SCR_016202 | SciCrunch Registry | Human Pancreas Analysis Program (HIRN-HPAP), PANC-DB | 2026-10-24 12:51:11 | 152 | |||||
|
University of Michigan Center for Gastrointestinal Research In Vivo Animal and Human Studies Core Resource Report Resource Website 1+ mentions |
University of Michigan Center for Gastrointestinal Research In Vivo Animal and Human Studies Core (RRID:SCR_015608) | biomaterial supply resource, material resource, tissue bank | Core facility that consists of the following 4 distinct programs: In Vivo Small Animal Studies Program, Organoid/Enteroid Modeling Program, Biospecimens Banking Service, and Clinical Design and Statistics. | in vivo, animal and human studies, gastrointestinal research |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Michigan Center for Gastrointestinal Research is organization facet of: University of Michigan Center for Gastrointestinal Research |
digestive disease | NIDDK P30 DK034933 | Available to affiliated researchers | SCR_015608 | SciCrunch Registry | 2026-10-24 12:51:11 | 1 | ||||||||
|
University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core Resource Report Resource Website |
University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core (RRID:SCR_015607) | biomaterial supply resource, material resource, tissue bank | Core whose services include anatomic pathology review of human and experimental animal tissues as well as consultation in the best approaches for such analyses, cost-effective and high quality processing and staining of formalin-fixed paraffin-embedded tissues, and making collections of human tissue and imaging technologies available to researchers. | tissue and cell imaging, gastrointestinal pathology, imaging technology, anatomic pathology |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Chicago Digestive Diseases Research Core Center is organization facet of: University of Chicago Digestive Diseases Research Core Center |
digestive disease | NIDDK P30 DK042086 | Available to the research community, Available to affiliated researchers, Available to DDRCC researchers | SCR_015607 | SciCrunch Registry | 2026-10-24 12:51:11 | 0 | ||||||||
|
MitoCarta Resource Report Resource Website 100+ mentions |
MitoCarta (RRID:SCR_018165) | data or information resource, database | Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria. | Gene, protein, mitochondrial protein, protein expression, data, human, mouse, RefSeq protein, analysis, mammalian mitochondra, FASEB list | Australian NHMRC ; Burroughs Wellcome Fund Career Award in the Biomedical Sciences ; Charles E. Culpeper Scholarship in Medical Science ; Howard Hughes Medical Institute ; NIDDK DK43351; NIDDK DK57521; NIGMS GM0077465 |
PMID:26450961 PMID:18614015 |
Free, Freely available | SCR_018165 | SciCrunch Registry | MitoCarta2.0 | 2026-10-24 12:51:13 | 208 |
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.
