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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-08-29 11:29:38 | 36 | |||||
|
OntoMate Resource Report Resource Website 1+ mentions |
OntoMate (RRID:SCR_018493) | service resource, software application, software resource, text-mining software | Software text mining tool aiding curation at Rat Genome Database. Ontology driven, concept based literature search engine developed at RGD. Tags abstracts with gene names, gene mutations, organism names and terms from ontologies vocabularies used at RGD. Open and fully customizable. | Curation, Rat Genome Database, text mining, ontology, concept based, literature search engine, search engine | is related to: Rat Genome Database (RGD) | NHLBI HL064541; NHLBI HL094271 |
PMID:25619558 | Free, Freely available | SCR_018493 | 2026-08-29 11:29:00 | 1 | ||||||||
|
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 | PROMIS, Patient Reported Outcomes Measurement Information System | 2026-08-29 11:30:59 | 3303 | ||||||
|
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; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-08-29 11:28:25 | 193 | |||||||
|
Michigan Imputation Server Resource Report Resource Website 1+ mentions |
Michigan Imputation Server (RRID:SCR_023554) | data access protocol, software resource, web service | Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4. | Genotype imputation, whole genotype imputation workflow, parallelization of computationally intensive tasks, | is related to: MINIMAC | Austrian Science Fund ; European Community Seventh Framework Programme ; NHGRI HG000376; NHGRI HG007022; NHLBI HL117626; NIA ; NIDA R01DA037904 |
PMID:27571263 | Free, Freely available | https://github.com/genepi/imputationserver | SCR_023554 | 2026-08-29 11:28:20 | 9 | |||||||
|
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; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-08-29 11:28:21 | 16 | |||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | data or information resource, data repository, database, service resource, storage service resource | A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data. | data sharing, collaboration, data management, analysis, genome, phenotype, crowd sourcing, open data, provenance, resource management, annotation, authoring, markup, r, python, java, command-line, cloud, FASEB list |
is used by: NF Data Portal is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: clearScience is related to: Exemplar Microscopy Images of Tissues has parent organization: Sage Bionetworks |
Cancer, Normal, Cardiovascular disease, Floppy hat syndrome | Life Sciences Discovery Fund ; NCI ; NHLBI ; Alfred P. Sloan Foundation |
The community can contribute to this resource | nlx_151983, DOI:10.17616/R3B934, r3d100011894, DOI:10.7303 | https://doi.org/10.17616/R3B934, https://doi.org/10.48550/arxiv.1506.00272, https://doi.org/10.7303/, https://dx.doi.org/10.7303, https://doi.org/10.17616/R3B934 | SCR_006307 | 2026-08-29 11:27:50 | 1104 | |||||
|
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 ; NIH Office of the Director U42 OD011140 |
Public, To investigators, Application required | nif-0000-12086 | SCR_006855 | National Swine Resource Research Center | 2026-08-29 11:27:36 | 79 | ||||||
|
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 | 2026-08-29 11:24:48 | 3040 | ||||||||
|
Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION) Resource Report Resource Website |
Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study (ACCORDION) (RRID:SCR_014373) | ACCORDION | data or information resource, data set, portal, topical portal | A prospective, observational follow-up study of at least 8000 participants who were treated and followed in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) Trial. Treatment in ACCORD ended in 2009 and ACCORDION is designed to further elucidate the long-term effects of the ACCORD treatment strategies and provide additional data on the relationships among various cardiovascular and diabetic risk factors. | follow up, long term effect, treatment strategy, accord, cardiovascular risk factor, diabetic risk factor |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources has parent organization: Wake Forest School of Medicine; North Carolina; USA |
Type 2 diabetes | NHLBI | ACCORD study data and biospecimens are Now available in the NHLBI Biological Specimen and Data Repository Information Coordinating Center | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx https://www.accordionstudy.org/public/docs/ACCORDION%20Protocol%2003-18-2011-%20FINAL.pdf https://biolincc.nhlbi.nih.gov/studies/accord/?q=ACCORD | SCR_014373 | Action to Control Cardiovascular Disease Risk in Diabetes Follow-up Study | 2026-08-29 11:24:54 | 0 | |||||
|
BioDepot-workflow-builder Resource Report Resource Website 1+ mentions |
BioDepot-workflow-builder (RRID:SCR_017402) | Bwb | data processing software, software application, software resource, workflow software | Software tool to create and execute reproducible bioinformatics workflows using drag and drop interface. Graphical widgets represent Docker containers executing modular task. Widgets are linked graphically to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains form-based user interface to facilitate parameter entry and console to display intermediate results. | bioinformatics, big, data, workflow, reproducible, Docker | NHGRI U24HG012674; NHLBI U54 HL127624; NIAID R03AI159286; NIGMS R01 GM126019 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-08-29 11:28:11 | 2 | ||||||||
|
SCDE Resource Report Resource Website 10+ mentions |
SCDE (RRID:SCR_015952) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.) | statistic, single, cell, rna, seq, rnaseq, differential, analysis, pathway, gene, geneset, dispersion, overdispersion, bayesian, expression, magnitude | Leukemia and Lymphoma Research UK ; Leukemia and Lymphoma Society ; NHLBI R01 HL097794; NIA K25 AG037596; NIDDK R01 DK050234 |
PMID:24836921 | Free, Available for download | SCR_015952 | 2026-08-29 11:28:06 | 32 | |||||||||
|
L1000 Characteristic Direction Signature Search Engine Resource Report Resource Website 1+ mentions |
L1000 Characteristic Direction Signature Search Engine (RRID:SCR_016177) | L1000CDS2 | data access protocol, data or information resource, data set, database, service resource, software resource, web service | LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction. | signature, gene, dataset, ligand, characteristic, expression, benchmark |
is related to: LINCS Joint Project - Breast Cancer Network Browser has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U54 CA189201; NHLBI U54 HL127624 |
PMID:28413689 | Free, Freely available | SCR_016177 | 2026-08-29 11:25:08 | 8 | |||||||
|
Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | data or information resource, data processing software, data visualization software, database, software application, software resource, web application | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NCI U54 CA189201; NHLBI U54 HL127624; NIGMS R01 GM098316 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-08-29 11:25:33 | 142 | |||||||||
|
AbundantOTU+ Resource Report Resource Website 1+ mentions |
AbundantOTU+ (RRID:SCR_016527) | AbundantOTU | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset. | pyrosequencing, 16S, rRNA, gene, operational, taxonomic, unit, abundant, species, dataset |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
NHGRI R01 HG004908; NHLBI U01 HL09896001 |
PMID:22102981 | Free, Available for download, Freely available | SCR_016527 | AbundantOTU:Abundant Operational Taxonomic Unit, Abundant OTU, AbundantOTU+ | 2026-08-29 11:25:16 | 1 | ||||||
|
LINCS Project Resource Report Resource Website 50+ mentions |
LINCS Project (RRID:SCR_016486) | LINCS | consortium, data or information resource, database, organization portal, portal, project portal | Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center. | data integration, network biology, gene expression, L1000, MCF10A, MEMA, P100, LINCS program, LINCS project, systems biology, systems pharmacology, FASEB list |
is related to: Drug Gene Budger is related to: LINCS Joint Project - Breast Cancer Network Browser is related to: piNET |
cancer, heart disease, neurodegenerative disorder | NHGRI U54 HG008097; NHGRI U54 HG008098; NHGRI U54 HG008100; NHLBI U54 HL127365; NHLBI U54 HL127366; NHLBI U54 HL127624; NIH Common Fund ; NINDS U54 NS091046 |
PMID:29199020 | Free, Freely available | SCR_016487 | SCR_016486 | LINCS, Library of Integrated Network based Cellular Signatures, LINCS Program | 2026-08-29 11:25:46 | 56 | ||||
|
National Sleep Research Resource (NSRR) Resource Report Resource Website 50+ mentions |
National Sleep Research Resource (NSRR) (RRID:SCR_016576) | NSRR | data or information resource, organization portal, portal | System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community. | sleep, clinical, data, cohort, study, trial, dataset, visualization, exploration |
is recommended by: National Library of Medicine lists: Apnea, Bariatric surgery, and CPAP study lists: Sleep Heart Health Study lists: Honolulu-Asia Aging Study of Sleep Apnea lists: Cleveland Family Study lists: Cleveland Children's Sleep and Health Study lists: Best Apnea Interventions for Research (BestAIR) sleep study |
sleep apnea | NHLBI | PMID:29860441 | Free, Freely available, Registration required for membership | https://sleepdata.org/share, https://sleepdata.org/datasets | SCR_016576 | National Sleep Research Resource | 2026-08-29 11:25:18 | 88 | ||||
|
Sleep Disorder Knowledge Portal Resource Report Resource Website 10+ mentions |
Sleep Disorder Knowledge Portal (RRID:SCR_016611) | data or information resource, database, disease-related portal, portal, topical portal | Software platform for accelerating genetic discoveries for sleep disturbance and circadian traits. | genetic, discovery, sleep, disorder, circadian, trait |
is listed by: NIDDK Information Network (dkNET) has parent organization: Broad Institute of MIT and Harvard has parent organization: Massachusetts General Hospital |
Sleep disorder, Circadian traits | National Institute of Diabetes and Digestive and Kidney Diseases ; NHLBI |
Public, Free, Google log in required | SCR_016611 | 2026-08-29 11:25:19 | 23 | ||||||||
|
Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | data or information resource, disease-related portal, portal, topical portal | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NCRR M01 RR00080; NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-08-29 11:25:19 | 4 | ||||||
|
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 | 2026-08-29 11:25:22 | 25 |
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.
