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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource | 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 RM1 HG009490; NIBIB R01 EB022376; NIGMS R35 GM118062; NIGMS R35 GM118158; NIDDK R03 DK109232; NHLBI P01 HL32262; NHGRI R00 HG008399; NIDDK P30 DK049216; NHLBI R01 HL119099; NHGRI R01 HG005085 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2 https://github.com/pinellolab/CRISPResso |
SCR_021538 | CRISPResso2 | 2026-02-16 09:50:04 | 21 | |||||||
|
National Longitudinal Mortality Study Resource Report Resource Website 10+ mentions |
National Longitudinal Mortality Study (RRID:SCR_008946) | NLMS | data set, data or information resource | A database based on a random sample of the noninstitutionalized population of the United States, developed for the purpose of studying the effects of demographic and socio-economic characteristics on differentials in mortality rates. It consists of data from 26 U.S. Current Population Surveys (CPS) cohorts, annual Social and Economic Supplements, and the 1980 Census cohort, combined with death certificate information to identify mortality status and cause of death covering the time interval, 1979 to 1998. The Current Population Surveys are March Supplements selected from the time period from March 1973 to March 1998. The NLMS routinely links geographical and demographic information from Census Bureau surveys and censuses to the NLMS database, and other available sources upon request. The Census Bureau and CMS have approved the linkage protocol and data acquisition is currently underway. The plan for the NLMS is to link information on mortality to the NLMS every two years from 1998 through 2006 with research on the resulting database to continue, at least, through 2009. The NLMS will continue to incorporate data from the yearly Annual Social and Economic Supplement into the study as the data become available. Based on the expected size of the Annual Social and Economic Supplements to be conducted, the expected number of deaths to be added to the NLMS through the updating process will increase the mortality content of the study to nearly 500,000 cases out of a total number of approximately 3.3 million records. This effort would also include expanding the NLMS population base by incorporating new March Supplement Current Population Survey data into the study as they become available. Linkages to the SEER and CMS datasets are also available. Data Availability: Due to the confidential nature of the data used in the NLMS, the public use dataset consists of a reduced number of CPS cohorts with a fixed follow-up period of five years. NIA does not make the data available directly. Research access to the entire NLMS database can be obtained through the NIA program contact listed. Interested investigators should email the NIA contact and send in a one page prospectus of the proposed project. NIA will approve projects based on their relevance to NIA/BSR''s areas of emphasis. Approved projects are then assigned to NLMS statisticians at the Census Bureau who work directly with the researcher to interface with the database. A modified version of the public use data files is available also through the Census restricted Data Centers. However, since the database is quite complex, many investigators have found that the most efficient way to access it is through the Census programmers. * Dates of Study: 1973-2009 * Study Features: Longitudinal * Sample Size: ~3.3 Million Link: *ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00134 | national, longitudinal, mortality, demographic, socio-economic, age, cause of death, death, death record, ethnicity, mortality rate, gender, marital status, race, late adult human, FASEB list |
is listed by: Inter-university Consortium for Political and Social Research (ICPSR) has parent organization: U.S. Census Bureau |
Aging | NCI ; NHLBI ; NIA ; National Center for Health Statistics ; U.S. Census Bureau |
Public | nlx_151861 | SCR_008946 | National Longitudinal Mortality Study (NLMS) | 2026-02-16 09:47:18 | 32 | |||||
|
SingleR Resource Report Resource Website 100+ mentions |
SingleR (RRID:SCR_023120) | software resource, software toolkit | Software R package for unbiased cell type recognition of scRNA-seq data. Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer cell of origin of each single cell independently. | unbiased cell type recognition, scRNA-seq data, reference transcriptomic datasets, pure cell types, infer cell of origin | UCSF Marcus Award ; NHLBI HL131560; UCSF Nina Ireland Program award ; NHLBI HL139897; NIAID |
PMID:30643263 | Free, Available for download, Freely available | https://github.com/dviraran/SingleR https://github.com/LTLA/SingleR |
SCR_023120 | Single-cell RNA-seq cell types Recognition | 2026-02-16 09:50:30 | 321 | |||||||
|
MR-PRESSO Resource Report Resource Website 50+ mentions |
MR-PRESSO (RRID:SCR_023697) | software resource, software toolkit | Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. | Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, | NIGMS R35 GM124836; NHLBI R01 HL139865; AstraZeneca ; Goldfinch Bio ; American Heart Association Cardiovascular Genome Phenome Discovery ; NIMH 1R01 MH094469; NIMH 1R01 MH107649; NHGRI 5U01 HG009088 |
PMID:29686387 | Free, Available for download, Freely available | SCR_023697 | Mendelian Randomization Pleiotropy RESidual Sum and Outlier | 2026-02-16 09:50:45 | 64 | ||||||||
|
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 | NIGMS R01 GM126019; NHLBI U54 HL127624; NHGRI U24HG012674; NIAID R03AI159286 |
DOI:10.1016/j.cels.2019.08.007 | Free, Available for download, Freely available | SCR_017402 | 2026-02-16 09:49:14 | 1 | ||||||||
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SCDE Resource Report Resource Website 10+ mentions |
SCDE (RRID:SCR_015952) | software application, data processing software, sequence analysis software, data analysis software, 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 | NIA K25 AG037596; NIDDK R01 DK050234; NHLBI R01 HL097794; Leukemia and Lymphoma Research UK ; Leukemia and Lymphoma Society |
PMID:24836921 | Free, Available for download | SCR_015952 | 2026-02-16 09:48:55 | 32 | |||||||||
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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 | NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-02-16 09:50:39 | 11 | |||||||
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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 | NHGRI HG007022; NHLBI HL117626; NHGRI HG000376; NIDA R01DA037904; Austrian Science Fund ; European Community Seventh Framework Programme ; NIA |
PMID:27571263 | Free, Freely available | https://github.com/genepi/imputationserver | SCR_023554 | 2026-02-16 09:50:38 | 8 | |||||||
|
OntoMate Resource Report Resource Website |
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 | 2026-02-16 09:49:30 | 0 | ||||||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/ https://github.com/poruloh/Eagle https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ |
SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-02-16 09:48:58 | 51 | |||||
|
VISTA Browser Resource Report Resource Website 50+ mentions |
VISTA Browser (RRID:SCR_011808) | software resource, software toolkit | Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. | Comparative genomics tools, genomic sequences, comparative analysis, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
Office of Biological and Environmental Research ; Office of Science ; US Department of Energy ; NHLBI |
PMID:15215394 | Free, Freely available | OMICS_00948, biotools:vista | http://genome.lbl.gov/vista/index.shtml https://bio.tools/vista |
SCR_011808 | VISTA, vista | 2026-02-16 09:48:09 | 87 | |||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | production service resource, service resource, data analysis service, analysis 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 | 2026-02-16 09:46:32 | 36 | |||||
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iDASH Resource Report Resource Website 1+ mentions |
iDASH (RRID:SCR_003524) | iDASH | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications. | data sharing, computing, biomedical, behavior, molecular, phenotyping, kawasaki disease, hematologic medication, individualized intervention, physical activity, phenotype, data set, image, cyberinfrastructure, schema, domain model, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: DataCite is related to: National Centers for Biomedical Computing is related to: NIH Data Sharing Repositories is related to: National Centers for Biomedical Computing has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIH Roadmap for Bioinformatics and Computational Biology ; NHLBI U54 HL108460 |
PMID:22081224 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:iDASH, https://api.datacite.org/dois?prefix=10.15147, nif-0000-38239 | https://bio.tools/iDASH | SCR_003524 | iDASH Repository, Integrating Data for Analysis Anonymization and SHaring | 2026-02-16 09:46:13 | 2 | ||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | data processing software, software application, software resource | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-02-16 09:46:31 | 120 | |||||
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CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | web service, data access protocol, database, software resource, 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 | 2026-02-16 09:50:57 | 16 | |||||||
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Predictomes Resource Report Resource Website 1+ mentions |
Predictomes (RRID:SCR_026691) | database, data or information resource | Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions. | Classifier-curated database, AlphaFold-modeled protein-protein interactions, interactive database, protein protein interactions, | NSF ; NHLBI HL098316 |
PMID:38645019 | Free, Freely available | SCR_026691 | 2026-02-16 09:51:13 | 2 | |||||||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software toolkit, source code, software resource | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-02-16 09:51:12 | 1 | |||||||||
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NetworkDataCompanion Resource Report Resource Website 1+ mentions |
NetworkDataCompanion (RRID:SCR_026532) | source code, software toolkit, software library, software resource | Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning. | TCGA and GTEx data analysis, TCGA data processing, filtering and mapping gene, normalization and cleaning, | NCI R35CA220523; NCI U24CA231846; NCI P50CA127003; NHGRI R01HG011393; NHGRI R01HG125975; NHLBI P01HL114501; NHLBI T32HL007427; NHLBI K01HL166376; American Lung Association |
PMID:39574772 | Free, Available for download, Freely available | SCR_026532 | 2026-02-16 09:51:11 | 1 | |||||||||
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ped-sim Resource Report Resource Website 1+ mentions |
ped-sim (RRID:SCR_026957) | software application, software resource, source code, simulation software | Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances. | Pedigree simulator, simulate pedigree structures, simulating relatives, sex-specific, sex averaged, genetic maps, | NIGMS R35 GM133805; Alfred P. Sloan Research Fellowship ; United States-Israel Binational Science Foundation ; NHLBI R01 HL0113323; NHLBI P01 HL045222; NIDDK R01 DK047482; NIDDK R01 DK053889; NIGMS T32 GM007617; NIGMS T32 GM083937; Wellcome Trust |
PMID:31860654 | Free, Available for download, Freely available | SCR_026957 | Ped-sim | 2026-02-16 09:51:17 | 2 | ||||||||
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BEERS2 Resource Report Resource Website |
BEERS2 (RRID:SCR_027287) | software application, software resource, source code, simulation software | Software for simulation of RNA-seq reads. Combines flexible and highly configurable design with detailed simulation of entire library preparation and sequencing pipeline and is designed to include effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. | RNA-seq reads, simulation of RNA-seq reads, | NCATS 5UL1TR000003; NHLBI R01HL155934; NHLBI R01HL147472; NIGMS DP2GM146251 |
PMID:38605641 | Free, Available for download, Freely available | SCR_027287 | 2026-02-16 09:51:21 | 0 |
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