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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | database, data or information resource | Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations. | genome, analysis, tissue, network, gene, machine, learning, biology | NIGMS R01 GM071966; NHGRI R01 HG005998; NHLBI U54 HL117798; NIGMS P20 GM103534; NHGRI T32 HG003284; NCI T32 CA009528; NIGMS P50 GM071508; US Department Of Health And Human Services HHSN272201000054C |
PMID:25915600 | Free, Public | SCR_016145 | GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), GIANT | 2026-08-04 09:43:50 | 74 | ||||||||
|
MitoCarta Resource Report Resource Website 100+ mentions |
MitoCarta (RRID:SCR_018165) | database, data or information resource | 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 | NIGMS GM0077465; NIDDK DK43351; NIDDK DK57521; Australian NHMRC ; Burroughs Wellcome Fund Career Award in the Biomedical Sciences ; Howard Hughes Medical Institute ; Charles E. Culpeper Scholarship in Medical Science |
PMID:26450961 PMID:18614015 |
Free, Freely available | SCR_018165 | MitoCarta2.0 | 2026-08-04 09:44:20 | 183 | ||||||||
|
Molecular Signatures Database Resource Report Resource Website 500+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | database, data or information resource | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NIH ; NIGMS ; NCI CA295532 |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-08-04 09:44:00 | 762 | ||||||
|
NETMAGE Resource Report Resource Website 1+ mentions |
NETMAGE (RRID:SCR_021843) | 2d spatial image, data or information resource, image | Web tool for automated generation of interactive disease-disease network visualizations given input PheWAS summary data. Given genetic associations from Phenome-Wide Association Study, disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes. | PheWAS, genetic associations from Phenome Wide Association Study, disease-disease network construction, phenotypes, shared genetic associations between phenotypes | has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA | NIGMS | DOI:10.1101/2020.10.27.357103 | Free, Available for download, Freely available | SCR_021851 | https://github.com/dokyoonkimlab/netmage | SCR_021843 | 2026-08-04 09:44:56 | 2 | ||||||
|
Knowledge Engineering from Experimental Design Resource Report Resource Website 1+ mentions |
Knowledge Engineering from Experimental Design (RRID:SCR_001238) | KEfED | software application, software resource | Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable. | experimental design, observation, interpretation, reasoning, experimental data, observational assertion, knowledge engineering, java |
is listed by: FORCE11 is related to: Bioscholar has parent organization: Biomedical Informatics Research Network |
NIGMS R01-GM083871; NIMH 1R01MH079068-01A2; NCRR 1 U24 RR025736-01 |
PMID:21859449 | Free, Available for download, Freely available | nif-0000-07745 | https://wiki.birncommunity.org/display/NEWBIRNCC/Knowledge+Engineering+from+Experimental+Design+%28%27KEfED%27%29 | SCR_001238 | 2026-08-04 09:40:20 | 1 | |||||
|
LONI MiND Resource Report Resource Website |
LONI MiND (RRID:SCR_004820) | MiND | software resource, service resource | The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework. | diffusion magnetic resonance imaging, metadata, dwi, dti, software interoperability, data sharing | has parent organization: David Geffen School of Medicine at UCLA; California; USA | NIH ; NCRR ; NIMH ; NCRR 1U54RR021813-01; NIGMS 5T32GM008042-25; NCRR P41 RR013642; NIMH R01 MH71940; NIBIB EB008432; NIBIB EB008281; NIBIB EB007813; NICHD HD050735 |
PMID:20206274 | nlx_143920 | http://mind.loni.ucla.edu/ | SCR_004820 | MiND: Metadata in NIfTI for DWI, Metadata in NIfTI for DWI | 2026-08-04 09:41:13 | 0 | |||||
|
Resource Identification Portal Resource Report Resource Website 10+ mentions |
Resource Identification Portal (RRID:SCR_004098) | RII Portal | portal, data or information resource | Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource. | antibody, organism, service resource, software resource, database, resource, identifier, citation, biomedical, publication, research resource identifier, rrid, ASWG |
uses: Antibody Registry uses: SciCrunch Registry uses: Mouse Genome Informatics (MGI) uses: Zebrafish Information Network (ZFIN) uses: Rat Genome Database (RGD) uses: WormBase uses: FlyBase recommends: SciCrunch Registry recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: Rat Genome Database (RGD) is recommended by: Neuroscience Information Framework is recommended by: SciCrunch Registry is related to: NIF Data Federation has parent organization: SciCrunch |
NIGMS R24 GM144308 | The community can contribute to this resource | nlx_158572 | SCR_004098 | Resource Identification Initiative Portal | 2026-08-04 09:41:03 | 19 | ||||||
|
Rhesus Macaque Atlases for Functional and Structural Imaging Studies Resource Report Resource Website 10+ mentions |
Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) | Rhesus Macaque Atlases | atlas, data or information resource | NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL. | magnetic resonance imaging, macaca mulatta, neuroscience, rhesus macaque, structure, neuroimaging, t1-weighted atlas, t2-weighted atlas, mri, brain, neuroanatomy | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | Aging | Intramural Research Program ; NCRR RR000167; NIA AG11915; NIA AG20013; NIGMS GM007507; NCRR RR00163; NIA AG029612 |
PMID:19059346 | NO LONGER AVAILABLE | nif-0000-33003 | SCR_008650 | 2026-08-04 09:42:11 | 10 | |||||
|
PEPATAC Resource Report Resource Website 1+ mentions |
PEPATAC (RRID:SCR_024758) | software resource, software toolkit | Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats. | ATAC-seq analysis pipeline, ATAC-seq data, analysis, serial alignments, | NHGRI RM1 HG007735; NIGMS R35 GM128636; Howard Hughes Medical Institute ; American Society of Hematology |
PMID:34859208 | Free, Available for download, Freely available | https://github.com/databio/PEPATAC/releases | SCR_024758 | 2026-08-04 09:45:35 | 2 | ||||||||
|
LABRAT Resource Report Resource Website 1+ mentions |
LABRAT (RRID:SCR_025006) | software application, software resource, source code | Software application to quantify usage of alternative polyadenylation and cleavage sites in RNAseq data and identify genes whose usage of these sites varies across experimental conditions. | quantify usage, alternative polyadenylation, cleavage sites, RNAseq data, identify genes, | NIGMS R35 GM133885; NIGMS R35 GM118051; RNA Bioscience Initiative at the University of Colorado Anschutz Medical Campus ; NIGMS T32 GM008730 |
DOI:10.1186/s12864-021-07781-1 | Free, Available for download, Freely available | SCR_025006 | Lightweight Alignment Based Resolution of Alternative Three prime ends | 2026-08-04 09:45:39 | 1 | ||||||||
|
MAGeCK Resource Report Resource Website 100+ mentions |
MAGeCK (RRID:SCR_025016) | data processing software, software application, software resource, data analysis software | Software tool to identify important genes from genome-scale CRISPR-Cas9 screens. Used for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. | identify genes, genome scale CRISPR-Cas9 screens, | NIGMS R01 GM099409; Dana-Farber Cancer Institute |
PMID:25476604 | Free, Available for download, Freely available | https://github.com/liulab-dfci/MAGeCK | SCR_025016 | Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout | 2026-08-04 09:45:42 | 182 | |||||||
|
CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | web service, software resource, data access protocol, database, data or information resource | Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions. | Mass Spectrometry contaminants, standardized negative controls, contaminant repository, AP-MS analysis, affinity purification, mass spectrometry data, | NIGMS 5R01GM94231; NIDA DP1DA026192; NHLBI HL112618-01; Canadian Institutes of Health Research ; government of Ontario ; Austrian Academy of Sciences ; Austrian Federal Ministry for Science and Research ; European Research Council ; Austrian Science Fund ; European Molecular Biology Organisation ; Netherlands Proteomics Center ; European Union 7th Framework Program ; Stowers Institute for Medical Research ; Human Frontier Science Program ; NCI R21 CA16006001A1 |
PMID:23921808 | Free, Freely available, | https://reprint-apms.org/ | SCR_025008 | CRAPome:Contaminant Repository for Affinity Purification | 2026-08-04 09:45:39 | 16 | |||||||
|
Cytoscape StringApp Resource Report Resource Website 10+ mentions |
Cytoscape StringApp (RRID:SCR_025009) | software application, software resource, source code | Software application for network analysis and visualization of proteomics data. Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains appearance and many of features of STRING, and integrates data from associated databases. | protein networks, network analysis and visualization, proteomics data, | is a plug in for: STRING | Novo Nordisk Foundation ; Danish Council for Independent Research ; NIGMS P41 GM103504; Chan Zuckerberg Initiative ; Silicon Valley Community Foundation |
PMID:30450911 | Free, Available for download, Freely available | https://github.com/RBVI/StringApp | SCR_025009 | stringApp | 2026-08-04 09:45:39 | 28 | ||||||
|
ReDU Resource Report Resource Website 1+ mentions |
ReDU (RRID:SCR_025105) | data access protocol, software resource, web service | Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE. | Mass Spectrometry data, find uniformly formatted public MS/MS data, formatted metadata, Global Natural Product Social Molecular Networking Platform, GNPS, find and re-analyze public Mass Spectrometry data, ReDU metadata standards, data validator, | has parent organization: University of California at San Diego; California; USA | NIGMS P41 GM103484; NCI R03 CA211211; NIGMS R01 GM107550; Sloan Foundation ; Gordon and Betty Moore Foundation ; American Society for Mass Spectrometry ; NSF ; Netherlands eScience Center ; FAPESP ; Krupp Endowed Fund ; US Office of Naval Research ; University of California ; San Diego Center for Microbiome Innovation SEED grants |
PMID:32807955 | Free, Freely available | SCR_025105 | Reanalysis of Data User | 2026-08-04 09:45:41 | 1 | |||||||
|
Find My Understudied Genes Resource Report Resource Website 1+ mentions |
Find My Understudied Genes (RRID:SCR_025047) | FMUG | software application, software resource, source code | Software data-driven tool to identify understudied genes and characterize their tractability. Users submit list of human genes and can filter these genes down based on list of factors. Code to generate Find My Understudied Genes app for Windows, iOS and macOS platforms. | has parent organization: Northwestern University; Illinois; USA | NIGMS T32GM008449; Northwestern University ; Moderna Inc ; NSF ; NAIAD U19AI135964; Simons Foundation ; NIA K99AG068544 |
DOI:10.7554/eLife.93429 | Free, Available for download, Freely available | https://github.com/amarallab/fmug | SCR_025047 | 2026-08-04 09:45:43 | 2 | |||||||
|
glmpca Resource Report Resource Website 1+ mentions |
glmpca (RRID:SCR_025517) | software resource, software toolkit, source code | Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data. | dimension reduction, non-normally distributed data, principal components analysis, | NCI T32CA009337; NHGRI R00HG009007; Chan-Zuckerberg Initiative ; NHGRI R01HG005220; NIGMS R01GM083084; NHGRI P41HG004059 |
PMID:31870412 | Free, Available for download, Freely available, | https://CRAN.R-project.org/package=glmpca | SCR_025517 | generalized version of principal components analysis | 2026-08-04 09:45:51 | 1 | |||||||
|
CellMinerCDB Resource Report Resource Website 10+ mentions |
CellMinerCDB (RRID:SCR_025649) | web application, software resource | Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements. | integrating cancer cell line pharmacogenomics, exploration and analysis of cancer cell line pharmacogenomic data, exploration and analysis, cancer cell line, pharmacogenomic data | is used by: National Cancer Institute Genomics and Pharmacology Core Facility | NIGMS P41 GM103504; NCI |
PMID:30553813 PMID:30553813 |
Free, Freely available, | SCR_025649 | , Cell Miner CDB, CellMiner Cross-Database, CellMinerCDB 1.2 | 2026-08-04 09:45:49 | 11 | |||||||
|
BioXTAS RAW Resource Report Resource Website 50+ mentions |
BioXTAS RAW (RRID:SCR_025769) | software application, software resource | Software tool as GUI based Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data.Small-angle scattering data reduction and analysis. Available on Windows, macOS (and OS X), and Linux. | reduction and analysis of small-angle X-ray solution scattering data, small-angle X-ray solution scattering data, | US Department of Energy ; NIGMS P30 GM138395 |
PMID:29021737 PMID:38322719 |
Free, Freely available, | SCR_025769 | BioXTAS RAW 2 | 2026-08-04 09:45:51 | 63 | ||||||||
|
Mustache Resource Report Resource Website 1+ mentions |
Mustache (RRID:SCR_026110) | software application, software resource, source code | Software tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps in high resolutions (10kbp all the way to 500bp and even more). Used to detect chromatin loops caused by interaction of DNA segments with variable size. | detect chromatin loops, interaction of DNA segments, Hi-C, Micro-C, contact maps, | NIGMS R35 GM128938 | PMID:32998764 | Free, Available for download, Freely available | SCR_026110 | Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation | 2026-08-04 09:45:54 | 5 | ||||||||
|
cooltools Resource Report Resource Website 10+ mentions |
cooltools (RRID:SCR_026118) | software resource, software toolkit, source code | Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation. | enables reproducible analysis, high-resolution contact frequency data, paired python API, | NIGMS R35 GM143116; NHGRI UM1 HG011536; NHGRI R01 HG003143 |
PMID:38709825 | Free, Available for download, Freely available | SCR_026118 | 2026-08-04 09:45:55 | 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 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.
