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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | data analysis software, data processing software, software application, software resource | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | Cancer Prevention Research Institute of Texas ; Google Research Award ; IBM University Challenge Award ; McNair Medical Institute Scholar Award ; NHGRI HG003067; NHGRI HG006193; NHLBI U01 HL130010; NIH Office of the Director DP2 OD008540; NSF PHY-1427654; NVIDIA Research Center Award ; PD Soros Fellowship ; President Early Career Award in Science and Engineering ; Welch Foundation |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-09-19 12:53:36 | 119 | ||||||||
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Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-09-19 12:53:43 | 6 | ||||||
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Drosophila RNAi Screening Center Resource Report Resource Website 1+ mentions |
Drosophila RNAi Screening Center (RRID:SCR_000733) | DRSC | data or information resource, database | Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays. | genome, screening, drosophila, fly, insect, rnai | has parent organization: Harvard University; Cambridge; United States | NIH Office of the Director R24 OD011176 | PMID:16381918 | nif-0000-02846 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, http://flyRNAi.org/cgi-bin/RNAi_screens.pl | SCR_000733 | Development of Validated Drosophila in vivo RNAi Models of Human Diseases | 2026-09-19 12:56:27 | 2 | |||||
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Microphysiology Systems Database Resource Report Resource Website 1+ mentions |
Microphysiology Systems Database (RRID:SCR_021126) | MPS-Db | data or information resource, database | Open source database used for analyzing and modeling compound interactions with human and animal organ models.Platform for experimental design, data management, and analysis, and to combine experimental data with reference data, to enable computational modeling. Resource for relating in vitro organ model data to multiple biochemical, preclinical, and clinical data sources on in vivo drug effects. | Compound interactions, human organ models, animal organ models, analyzing interactions, modeling interactions, |
is used by: NIH Heal Project is listed by: re3data.org |
NCATS UH3 TR00503; NIH Office of the Director S10 OD01226; U.S. Environmental Protection Agency |
PMID:28781990 | Free, Freely available | SCR_021126 | MPS database | 2026-09-19 12:57:38 | 4 | ||||||
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Resource for Genetic Epidemiology Research on Adult Health and Aging Resource Report Resource Website 1+ mentions |
Resource for Genetic Epidemiology Research on Adult Health and Aging (RRID:SCR_010472) | GERA | data or information resource, database | Human genetics data from an immense (78,000) and ethnically diverse population available for secondary analysis to qualified researchers through the database of Genotypes and Phenotypes (dbGaP). It offers the opportunity to identify potential genetic risks and influences on a broad range of health conditions, particularly those related to aging. The GERA cohort is part of the Research Program on Genes, Environment, and Health (RPGEH), which includes more than 430,000 adult members of the Kaiser Permanente Northern California system. Data from this larger cohort include electronic medical records, behavioral and demographic information from surveys, and saliva samples from 200,000 participants obtained with informed consent for genomic and other analyses. The RPGEH database was made possible largely through early support from the Robert Wood Johnson Foundation to accelerate such health research. The genetic information in the GERA cohort translates into more than 55 billion bits of genetic data. Using newly developed techniques, the researchers conducted genome-wide scans to rapidly identify single nucleotide polymorphisms (SNPs) in the genomes of the people in the GERA cohort. These data will form the basis of genome-wide association studies (GWAS) that can look at hundreds of thousands to millions of SNPs at the same time. The RPGEH then combined the genetic data with information derived from Kaiser Permanente''s comprehensive longitudinal electronic medical records, as well as extensive survey data on participants'' health habits and backgrounds, providing researchers with an unparalleled research resource. As information is added to the Kaiser-UCSF database, the dbGaP database will also be updated. | genotype, phenotype, genome-wide association study, saliva, dna, male, female, health condition, electronic medical record, single nucleotide polymorphism, adult human, late adult human, gene, genome |
has parent organization: NCBI database of Genotypes and Phenotypes (dbGap) has parent organization: University of California at San Francisco; California; USA |
Aging, Cardiovascular disease, Osteoarthritis, Depressive Disorder, Insomnia, Eye disease, Cancer, Diabetes | NIMH ; NIH Office of the Director ; NIA AG036607 |
Application required, Non-commercial, Data Use Certification Agreement | nlx_157735 | SCR_010472 | Genetic Epidemiology Research on Aging | 2026-09-19 12:57:21 | 9 | |||||
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Baylor College of Medicine Human Genome Sequencing Center Resource Report Resource Website 50+ mentions |
Baylor College of Medicine Human Genome Sequencing Center (RRID:SCR_013605) | BCM-HGSC | analysis service resource, production service resource, service resource | Center for high-throughput DNA sequence generation and the accompanying analysis. The sequence data generated by the center's machines are analyzed in a complex bioinformatics pipeline, and the data are deposited regularly in the public databases at the National Center for Biotechnology Information (NCBI). | next-generation sequencing, genetic variation, genome, dna sequence, FASEB list |
has parent organization: Baylor University; Texas; USA is parent organization of: Mercury is parent organization of: xAtlas |
NIH Office of the Director R24 OD011173 | nif-0000-10162 | SCR_013605 | Human Genome Sequencing Center, BCM HGSC | 2026-09-19 12:57:32 | 65 | |||||||
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National Natural Toxins Research Center Resource Report Resource Website 10+ mentions |
National Natural Toxins Research Center (RRID:SCR_002824) | VRC, NNTRC | access service resource, core facility, service resource | Center to provide global research, training, and resources that will lead to the discovery of medically important toxins found in venoms. The Viper Resource Center (VRC) is located in the Natural Toxins Research Center at Texas A&M University-Kingsville. | venom, venomous snake, snake, LD50, ED50, toxin, toxins, electrophoretic titration, enzyme, fibrinolytic, function, assay, cancer, cell, chromatography, compound, disintegrin, venom gland, hemorrhagic, integrin, metalloproteinases, polypeptide, protein, proteolytic, species, vendor, research training |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Texas A and M University-Kingsville; Texas; USA |
NIH Office of the Director P40 OD010960 | Free, Freely available | nif-0000-24966 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | http://ntrc.tamuk.edu/, https://www.tamuk.edu/artsci/departments/nntrc/index.html | SCR_002824 | Viper Resource Center | 2026-09-19 12:58:35 | 35 | ||||
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Tetrahymena Stock Center Resource Report Resource Website 50+ mentions |
Tetrahymena Stock Center (RRID:SCR_008362) | TSC | biomaterial supply resource, material resource | Centralized repository and distribution site for variety of Tetrahymena strains and species. Maintains diverse array of wild type, mutant, and genetically engineered strains of T. thermophila, the most commonly used laboratory species, and variety of other species derived from both laboratory maintained stocks and wild isolates. All stocks are stored in liquid nitrogen to maintain genetic integrity and prevent senescence. In addition to providing worldwide access to strains currently in collection, TSC continually upgrades collection by accepting deposition of newly developed laboratory strains and well characterized wild isolates collected from clearly defined natural sites. | RIN, Resource Information Network, eukaryota, genetics, biology, cell, cellular, culture, model, molecular, protozoan, repository, research, tetrahymena thermophila, RRID Community Authority |
is used by: Integrated Animals is listed by: Resource Information Network has parent organization: Cornell University; New York; USA |
NIH Office of the Director P40 OD010964 | nif-0000-25476 | http://vivo.cornell.edu/individual/vivo/individual27605 | SCR_008362 | Resource Center For Tetrahymena Thermophila | 2026-09-19 12:57:55 | 89 | ||||||
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Mutant Mouse Resource and Research Center - Jackson Laboratory Resource Report Resource Website 10+ mentions |
Mutant Mouse Resource and Research Center - Jackson Laboratory (RRID:SCR_016446) | MMRRC JAX, JAX MMRRC, JAX MMR | biomaterial supply resource, material resource | Center for mutant mouse research and distribution. The objectives of the JAX MMRRC are to: identify and evaluate biomedically-significant mice, import/acquire and archive mouse strains, distribute mouse strains, and operate a control program to ensure genetic stability. | mouse, mutation, clinical, research, biomedicine, genetics, gene, strain | is organization facet of: Mutant Mouse Resource and Research Center | NIH Office of the Director U42 OD010921 | SCR_016446 | JAX Mutant Mouse Resource and Research Center, Mutant Mouse Resource and Research Center - JAX, Jackson Laboratory MMRRC, Jackson Laboratory Mutant Mouse Resource and Research Center | 2026-09-19 12:58:15 | 23 | ||||||||
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Mutant Mouse Resource and Research Center - University of North Carolina Resource Report Resource Website 1+ mentions |
Mutant Mouse Resource and Research Center - University of North Carolina (RRID:SCR_016449) | UNC MMRRC, MMRRC UNC, MMRRC UNCCH | biomaterial supply resource, material resource | Center that is a mouse cryoarchive and distribution center, which incorporates research goals that synergize with and extend the value of the resource. The goals of the UNC Chapel Hill center are to streamline and improve operating procedures, establish a comprehensive cryoarchive, develop and disseminate computational tools for mouse genotyping, and examine the effect of paternal age and epigenetics on mutation rate. | mouse, cryogenic, mice, transgenic, knockout, genetic, mutant, mutation, epigenetics, research, animal | is organization facet of: Mutant Mouse Resource and Research Center | NIH Office of the Director U42 OD010924 | SCR_016449 | Mutant Mouse Resource and Research Center University of North Carolina, Mutant Mouse Resource and Research Center UNC, UNC Chapel Hill MMRRC, University of North Carolina Mutant Mouse Resource and Research Center, UNC Chapel Hill Mutant Mouse Resource and Research Center | 2026-09-19 12:58:15 | 3 | ||||||||
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University of Nebraska Medical Center Translational Mouse Model Core Facility Resource Report Resource Website |
University of Nebraska Medical Center Translational Mouse Model Core Facility (RRID:SCR_016452) | biomaterial supply resource, material resource | Center that conducts and supports research with mouse models. It also supplies mouse models to researchers. | mouse, mice, translation, biomedicine | has parent organization: University of Nebraska; Nebraska; USA | NIH Office of the Director R24 OD018546 | SCR_016452 | Center for Humanized Mice, UNMC Translational Mouse Model Core Facility | 2026-09-19 12:58:15 | 0 | |||||||||
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | data processing software, image processing software, software application, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; Multidisciplinary University Research Initiative Army Research Office ; NIAID R01AI130303; NIGMS F31GM116517; NIGMS P41GM10371; NIH Office of the Director DP2OD006514; NIMH P50MH09427; NIMH R01MH110932; NINDS R01NS076467; NINDS R01NS095367; NINDS U01NS090449; NSF NSF-1707316 |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | 2026-09-19 12:55:27 | 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 | software resource, web application | Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries. | Transcription Factor, gene sets, transcription factor enrichment analysis, TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, TF-gene co-occurrence, prediction of correct upstream, | NCI U24CA224260; NHLBI U54HL127624; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-09-19 12:55:31 | 193 | |||||||
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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 | NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-09-19 12:55:36 | 16 | |||||||
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GeneRanger Resource Report Resource Website |
GeneRanger (RRID:SCR_023622) | data access protocol, software resource, web service | Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types. | explore single gene expression, gene expression across tissues and cell types, gene expression, |
is related to: TargetRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA224260; NCI U24CA264250; NCI U24CA271114; NIDDK R01DK131525; NIDDK RC2DK131995; NIH Office of the Director OT2OD030160 |
PMID:37166966 | Free, Freely available | SCR_023622 | 2026-09-19 12:55:36 | 0 | ||||||||
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TargetRanger Resource Report Resource Website 1+ mentions |
TargetRanger (RRID:SCR_023621) | data access protocol, software resource, web service | Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines. | identify targets, identify genes, user inputted RNA-seq samples, target cells, proteomics data, human cells, |
is related to: GeneRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA224260; NCI U24CA264250; NCI U24CA271114; NIDDK R01DK131525; NIDDK RC2DK131995; NIH Office of the Director OT2OD030160 |
PMID:37166966 | Free, Freely available | https://maayanlab.github.io/Workshop.io/generanger | SCR_023621 | 2026-09-19 12:55:36 | 2 | |||||||
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CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | data access protocol, service resource, software resource, web service | Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design. | Design tool, CRISPR mediated gene editing, gene repression, gene activation, guide RNA design, genome, automated genome, sgRNA design, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
FANEDD ; NIDA R01 DA036858; NIDCR ; NIH Office of The Director ; NIH Office of the Director OD017887; NSFC |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | CRISP-Editing, Repression and Activation | 2026-09-19 12:53:57 | 13 | |||||
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Fitness Browser Resource Report Resource Website 1+ mentions |
Fitness Browser (RRID:SCR_018981) | data access protocol, data or information resource, software resource, web service | Web tool for browsing genome wide fitness experiments for diverse bacteria from Deutschbauer lab, the Arkin lab, and collaborators. Collection of mutant phenotypes for bacterial genes of unknown function. | Genome browser, bacteria, mutant phenotype, bacterial genes, unknown function, data | has parent organization: University of California at Berkeley; Berkeley; USA | NCRR S10 RR027303; NCRR S10 RR029668; NIH Office of the Director OD018174; Office of Science of the US Department of Energy |
PMID:29769716 | Free, Freely available | SCR_018981 | 2026-09-19 12:55:18 | 9 | ||||||||
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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, cell repository, material resource, organism supplier | Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. | RIN, Resource Information Network, pig, fetal fibroblast, live animal, tissue, fibroblast, fetus, genetically modified pig, biomaterial manufacture, genome, genotyping, genetics, reproduction, breeding, health monitoring, cryopreservation, phenotyping, consulting, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NHLBI ; NIAID ; NIH Office of the Director U42 OD011140 |
Public, To investigators, Application required | nif-0000-12086 | SCR_006855 | National Swine Resource Research Center | 2026-09-19 12:55:09 | 79 | ||||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, software resource, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | Austrian Science Fund ; German Research Foundation ; Korean Government ; Mexican National Council of Science and Technology ; NIAID R01AI167860; NIA U19AG063744; NIDDK T32DK007202; NIDDK U01DK119702; NIDDK U24DK133658; NIGMS 1DP2GM137413; NIGMS 1R01GM132649; NIGMS R01GM107550; NIGMS R35GM142938; NIH Office of the Director S10 OD021750; NLM 1R01LM013115; NSF ; Research Council of Norway ; Sao Paulo Research Foundation |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-09-19 12:55:47 | 7 |
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