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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OntoMate Resource Report Resource Website |
OntoMate (RRID:SCR_018493) | software application, software resource, service 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 | 2026-08-04 09:44:21 | 0 | ||||||||
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ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | web application, software resource | 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, | NHLBI U54HL127624; NCI U24CA224260; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-08-04 09:45:11 | 108 | |||||||
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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 | 2026-08-04 09:45:18 | 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 | 2026-08-04 09:45:17 | 8 | |||||||
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CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | data processing software, data analysis software, software resource, sequence analysis software, software application, software toolkit | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI 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 | 2026-08-04 09:44:50 | 21 | |||||||
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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, material resource, cell repository, 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 |
NIH Office of the Director U42 OD011140; NIAID ; NHLBI |
Public, To investigators, Application required | nif-0000-12086 | SCR_006855 | National Swine Resource Research Center | 2026-08-04 09:41:42 | 79 | ||||||
|
Synapse Resource Report Resource Website 1000+ mentions |
Synapse (RRID:SCR_006307) | Synapse | storage service resource, data repository, service resource, database, data or information 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 | 2026-08-04 09:41:34 | 1002 | |||||
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SCDE Resource Report Resource Website 10+ mentions |
SCDE (RRID:SCR_015952) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:43:46 | 32 | |||||||||
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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 | 2026-08-04 09:44:12 | 1 | ||||||||
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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) | 2026-08-04 09:42:16 | 32 | |||||
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Public Expression Profiling Resource Resource Report Resource Website 10+ mentions |
Public Expression Profiling Resource (RRID:SCR_007274) | PEPR | database, data or information resource | An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ). | microarray, expression profiling, affymetrix, metadata standard, gene, time series, data sharing, visualization, data mining, platform, blood, cell, cancer, bone, brain, eye, gut, heart, kidney, liver, lung, muscle, spinal cord, spleen, analysis |
is listed by: OMICtools is related to: Gene Expression Omnibus |
NINDS ; United States Department of Defense ; NHGRI ; NHLBI |
PMID:14681485 PMID:14596642 |
Public, Account required, (to download, For the analysis and visualization tools), The community can contribute to this resource | nif-0000-00014, OMICS_00776 | SCR_007274 | 2026-08-04 09:41:48 | 16 | ||||||
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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 | |||||||
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Signaling Pathways Project Resource Report Resource Website 10+ mentions |
Signaling Pathways Project (RRID:SCR_018412) | SPP | database, data or information resource | Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available. | Data integration, genetic database, gene regulatory network, cell signalling, cellular signalling network, transcriptomic data, manualy curated, cistromic data, cellular receptor, enzyme, transcrptomic factor, mammalian cellular signaling pathway, data mining strategy, dataset, , bio.tools |
is used by: Hypothesis Center is listed by: Debian is listed by: bio.tools works with: Gene Expression Omnibus (GEO) works with: NCBI Sequence Read Archive (SRA) |
NIDDK DK097771; NIDDK DK097748; NIDDK DK48807; NIDDK DK107535; NIDDK DK56338; NIDDK DK095686; NIDDK DK105126; NCI CA125123; NHLBI HL127624; Dan L. Duncan NCI Comprehensive Cancer Center at Baylor College of Medicine ; CPRIT RP150578 |
PMID:31672983 | Free, Freely available | r3d100013650, biotools:Signaling_Pathways_Project | https://bio.tools/Signaling_Pathways_Project, https://doi.org/10.17616/R31NJN0Y | https://www.signalingpathways.org | SCR_018412 | 2026-08-04 09:44:20 | 30 | ||||
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Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) Resource Report Resource Website 100+ mentions |
Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) (RRID:SCR_013142) | BioLINCC | database, data or information resource | Repository that serves to coordinate searches across data and biospecimen collections from participants in numerous clinical trials and epidemiologic studies and to provide an electronic means for requests for additional information and the submission of requests for collections. The collections, comprising data from more than 80 trials or studies and millions of biospecimens, are available to qualified investigators under specific terms and conditions consistent with the informed consents provided by the individual study participants. Some datasets are presented with studies and supporting materials to facilitate their use in reuse and teaching. Datasets support basic research, clinical studies, observational studies, and demonstrations. Researchers wishing to apply to submit biospecimen collections to the NHLBI Biorepository for sharing with qualified investigators may also use this website to initiate that process. | cardiovascular, pulmonary, hematology, clinical, clinical trial, blood, lung, heart, biological specimen, health, disease, medicine, epidemiology, epidemiologic study, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: DataCite is listed by: NIH Data Sharing Repositories is listed by: Connected Researchers is listed by: NIDDK Information Network (dkNET) is related to: NIH Data Sharing Repositories is related to: Framingham Heart Study has parent organization: National Heart Lung and Blood Institute |
NHLBI | Public, The community can contribute to this resource | r3d100010834, nlx_151758 | https://biolincc.nhlbi.nih.gov/, https://biolincc.nhlbi.nih.gov/ | SCR_013142 | NHLBI Biorepository | 2026-08-04 09:43:09 | 250 | |||||
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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 | ||||||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software resource, software toolkit, source code | 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 | 2026-08-04 09:46:02 | 1 | |||||||||
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NetworkDataCompanion Resource Report Resource Website 1+ mentions |
NetworkDataCompanion (RRID:SCR_026532) | software toolkit, software resource, source code, software library | 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 | 2026-08-04 09:46:00 | 1 | |||||||||
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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 | 2026-08-04 09:46:03 | 2 | |||||||||
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ped-sim Resource Report Resource Website 1+ mentions |
ped-sim (RRID:SCR_026957) | simulation software, software application, software resource, source code | 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 | 2026-08-04 09:46:06 | 2 | ||||||||
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BEERS2 Resource Report Resource Website |
BEERS2 (RRID:SCR_027287) | simulation software, software application, software resource, source code | 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 | 2026-08-04 09:46:10 | 0 |
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