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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility Resource Report Resource Website |
University of Manitoba Department of Plant Science Bio Information Technologies Lab Core Facility (RRID:SCR_017177) | University of Manitoba BIT Core Facility | data analysis service, analysis service resource, access service resource, software resource, core facility, production service resource, service resource, data or information resource | BIT Core at University of Manitoba, Manitoba, Canada, provides bioinformatics services, resources and collaborations. Support for Genome assembly and annotation, Microarray and Transcriptomics, Systems Biology and Pathway analysis, Databases, Data pipelines, Bioinformatics software, Custom software and programming, Project Wikis, Lab group computer management. | bioinformatics, genome, assembly, microarray, transcriptomics, pathway, data, analysis, management | Restricted | SCR_017177 | University of Manitoba, BIT, Bio Information Technologies Lab, Fritensky Lab, Canada, Department of Plant Science | 2026-08-04 09:44:08 | 0 | |||||||||
|
Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | portal, data set, project portal, database, data or information resource | Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data. | Spienza University of Rome, Cineca, RNA seq, transcriptome, data, brain, mouse, stress, gene, expresison | Free, Available for download, Freely available | SCR_017572 | 2026-08-04 09:44:11 | 1 | |||||||||||
|
DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | data processing software, software application, software resource, data analysis software | Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data. | Manifold interpretation, scRNAseq data, relevance scores infering, transcriptional program, psuedotemporal ordering, disease status, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:drivaer | https://bio.tools/drivaer | SCR_019076 | Driving transcriptional programs using AutoEncoder based Relevance scores | 2026-08-04 09:44:28 | 1 | |||||||
|
Epigenomics Workflow on Galaxy and Jupyter Resource Report Resource Website 1+ mentions |
Epigenomics Workflow on Galaxy and Jupyter (RRID:SCR_017544) | data processing software, data analysis software, workflow, software resource, training material, software application, narrative resource, data or information resource | Software tool as epigenomics analysis pipeline for analysis of ChIP-Seq and RNA-Seq data using Docker images containing Galaxy and Jupyter. | Epigenomic, analysis, pipeline, ChIP-Seq, RNA-Seq, data, Galaxy, Jupyter, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Estatal de Investigación of Spain SEV-2016-0672 (2017-2021) | Free, Available for download, Freely available | biotools:Epigenomics_Workflow_on_Galaxy_and_Jupyter | https://zenodo.org/record/3298029, https://bio.tools/Epigenomics_Workflow_on_Galaxy_and_Jupyter | SCR_017544 | REA pipeline | 2026-08-04 09:44:09 | 2 | ||||||
|
OpticalMapping.info Resource Report Resource Website |
OpticalMapping.info (RRID:SCR_017146) | topical portal, portal, software resource, data or information resource | Platform to provide tutorials and resources in experimental design and data analysis to researchers interested in using optical mapping data. | platform, tutorial, experimental, design, data, analysis, optical, mapping, structural, labelling, pattern, long, DNA, molecule, fluorescent, signal, capture | Free, Freely available | SCR_017146 | 2026-08-04 09:44:05 | 0 | |||||||||||
|
Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data processing software, software application, software resource, data analysis software | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus, https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst | SCR_021644 | 2026-08-04 09:44:53 | 2 | |||||||
|
Gene Expression Omnibus (GEO) Resource Report Resource Website 10000+ mentions |
Gene Expression Omnibus (GEO) (RRID:SCR_005012) | GEO | storage service resource, data repository, service resource, database, data or information resource | Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries. | gold standard, genomics, data, repository, microarray, mRNA, DNA, protein, analysis, SAGE, mass spectrometry, dataset |
is used by: ChIPseeker is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Allen Institute for Brain Science has parent organization: NCBI works with: shinyGEO works with: Drug Gene Budger works with: Signaling Pathways Project works with: GEN3VA |
National Library of Medicine | PMID:23193258 PMID:21097893 PMID:18940857 PMID:17160034 PMID:17099226 PMID:16939800 PMID:16888359 PMID:15608262 PMID:11752295 |
r3d100010283, nif-0000-00142, nlx_96903, OMICS_01030, SCR_007303 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds, http://www.ncbi.nlm.nih.gov/geo/, https://doi.org/10.17616/R33P44 | http://www.ncbi.nlm.nih.gov/gds | SCR_005012 | Gene Expression Omnibus (GEO), Entrez GEO DataSets, Gene Expression Data Sets, Gene Expression Omnibus, GEO, NCBI GEO DataSets, GEO DataSets, Gene Expression Omnibus DataSets | 2026-08-04 09:41:16 | 11944 | ||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, software resource, service resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-08-04 09:44:27 | 3 | |||||||
|
Hetindel Resource Report Resource Website 1+ mentions |
Hetindel (RRID:SCR_018922) | data processing software, software application, software resource, data analysis software | Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels. | Genomic insertions identification, genomic deletions identification, indel, heterozygous sequencing data, alleles, mutation, heterozygous indel, data | has parent organization: Max Planck Institute for Developmental Biology; Tubingen; Germany | Free, Available for download, Freely available | SCR_018922 | 2026-08-04 09:44:29 | 1 | ||||||||||
|
Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | data processing software, data analysis software, software resource, software application, software toolkit | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
UK Medical Research Council ; European Research Council Starting Grant ; European Research Council Advanced Grant |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2026-08-04 09:44:27 | 7 | |||||||
|
CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | data processing software, data analysis software, software resource, software application, software toolkit | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2026-08-04 09:44:30 | 22 | |||||||||
|
COVID-19 Data Repository Resource Report Resource Website 1+ mentions |
COVID-19 Data Repository (RRID:SCR_019105) | portal, topical portal, storage service resource, disease-related portal, data repository, service resource, data or information resource | Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings. | COVID-19, impact data, novel coronavirus global pandemic, novel coronavirus, data |
uses: DataCite is related to: OpenICPSR has parent organization: University of Michigan; Ann Arbor; USA |
COVID-19 | Free, Freely available | https://doi.org/10.3886, https://dx.doi.org/10.3886 | SCR_019105 | 2026-08-04 09:44:29 | 1 | ||||||||
|
Clinical Trials Viewer Resource Report Resource Website |
Clinical Trials Viewer (RRID:SCR_019230) | data access protocol, software resource, web service | Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set. | Drug, clinical data, clinical trial data, data, ClinicalTrials.gov data, FDA submission, FDA documents, FDA dataset |
is related to: ClinicalTrials.gov has parent organization: McGill University; Montreal; Canada |
Free, Available for download, Freely available | SCR_019230 | 2026-08-04 09:44:31 | 0 | ||||||||||
|
Urinary Stone Disease Research Network Resource Report Resource Website |
Urinary Stone Disease Research Network (RRID:SCR_019059) | USDRN | topical portal, portal, disease-related portal, data or information resource | Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies. | Urinary stone, kidney stone, kidney, treatment, prevention, urologist, nephrologist, pediatrician, clinical trial, data |
is related to: Duke University School of Medicine; North Carolina; USA is related to: University of Pennsylvania; Philadelphia; USA is related to: University of Texas System; Texas; USA is related to: Washington University in St. Louis; Missouri; USA is related to: University of Washington; Seattle; USA |
Kidney stones | NIH ; NIDDK |
Free, Freely available | SCR_019059 | 2026-08-04 09:44:28 | 0 | |||||||
|
Calliope calcium imaging processing package Resource Report Resource Website 1+ mentions |
Calliope calcium imaging processing package (RRID:SCR_021213) | data processing software, software resource, software application, image processing software, software toolkit | Software package for image processing for MATLAB. Used for processing of calcium imaging data. | Image processing, data, calcium imaging data, calcium imaging |
is used by: IRIS two photon acquisition package is related to: MATLAB |
Swiss National Science Foundation ; Novartis Research Foundation |
DOI:10.1016/j.cell.2017.05.023 | Free, Available for download, Freely available | SCR_021213 | 2026-08-04 09:44:45 | 1 | ||||||||
|
Matlab Health and Socio-Economic Survey Resource Report Resource Website |
Matlab Health and Socio-Economic Survey (RRID:SCR_008942) | MHSS | data set, data or information resource | A data set of the health and socioeconomic factors that affect the elderly in Matlab, a region of rural Bangladesh. The survey captures measurements and statistics such as adult survival, health status, health care utilization, resource flows between generations and the impact of community services and infrastructure on adult health care. Data was collected through surveys that touch on four topics: household and individual information; determinants of natural fertility; migration out of the community; and community and provider survey of healthcare and education infrastructure. | survey, bangladesh, adult, birth control, child development, culture, fertility, health behavior, health care, health care facility, health care service, health services utilization, health status, household budget, household expenditure, housing condition, infant feeding, reproductive history, school, social network, socioeconomic status, traditional medicine, women's health care, socioeconomic, behavior, family, community, household, woman, female, pregnancy status, outmigrant, family planning, international, questionnaire, clinical, interview, research, data |
is listed by: Inter-university Consortium for Political and Social Research (ICPSR) has parent organization: National Archive of Computerized Data on Aging (NACDA) |
Aging | NIA P01AG11952 | Public, Data and documentation may be used for academic and public policy research purposes only | nlx_151854 | SCR_008942 | Matlab Health and Socioeconomic Survey, Matlab Health and Socioeconomic Survey (MHSS), Matlab Health and Socio-Economic Survey (MHSS) | 2026-08-04 09:42:14 | 0 | |||||
|
Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center Resource Report Resource Website |
Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) | BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics. | RT PCR, transcriptome, epigenome, metabolomics, profiling, assay, protein, expression, pathway, data, bioinformatics, analysis, next, generation, sequencing, human, mouse, array, tissue, imaging |
is listed by: Eagle I is related to: Beth Israel Deaconess Medical Center Labs and Facilities is related to: Harvard University Labs and Facilities has parent organization: Harvard University; Cambridge; Massachusetts |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156126 | http://www.bidmcgenomics.org/ | SCR_009668 | Beth Israel Deaconess Medical Center, BIDMC | 2026-08-04 09:42:27 | 0 | ||||||
|
Montana State University Bioinformatics Core Facility Resource Report Resource Website |
Montana State University Bioinformatics Core Facility (RRID:SCR_009937) | access service resource, core facility, 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 | 2026-08-04 09:42:31 | 0 | |||||||
|
Washington University School of Medicine Knight ADRC Request Center Resources Core Facility Resource Report Resource Website 1+ mentions |
Washington University School of Medicine Knight ADRC Request Center Resources Core Facility (RRID:SCR_025254) | access service resource, core facility, service resource | Provides on request resources including Data: clinical and cognitive measures as well as MRI and amyloid imaging scans; Tissue: frozen brain tissue, paraffin brain sections, antemortem CSF, DNA, fibroblast, dermal fibroblasts, plasma (fasting and non-fasting) and iPSC; Participants: eligible participants may be invited to enroll in research of other investigators after appropriate review. Researchers can use the request portal to review Center guidelines and policies; view available data and tissue; access data tables and codebooks; and submit request for resources. | ABRF, Alzheimer research, Data, OASIS, Biospecimen, tissue, imaging, |
is listed by: ABRF CoreMarketplace has parent organization: Washington University School of Medicine Knight Alzheimers Disease Research Center has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Alzheimer disease, dementia | NIA P30AG066444; NIA P01AG026276; NIA U19 AG0032438; NIA P01AG003991 |
ABRF_2734 | https://coremarketplace.org/?FacilityID=2734&citation=1 | SCR_025254 | ADRC Request Center Resources | 2026-08-04 09:45:43 | 2 | ||||||
|
DSigDB Resource Report Resource Website 50+ mentions |
DSigDB (RRID:SCR_026202) | database, data or information resource | Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets. | gene sets, quantitative inhibition, drug induced, gene expression changes, data, drugs, compounds, | NCI P30CA046934; NCI P50CA058187 |
PMID:25990557 | Free, Freely available, | SCR_026202 | , Drug Signatures Database, drug SIGnatures DataBase | 2026-08-04 09:45:56 | 82 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
