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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Vietnam Era Twin Registry Resource Report Resource Website 1+ mentions |
Vietnam Era Twin Registry (RRID:SCR_008807) | VET Registry | data or information resource, patient registry, people resource, portal, topical portal | The Vietnam Era Twin (VET) Registry is a closed cohort composed of approximately 7,000 middle-aged male-male twin pairs both of whom served in the military during the time of the Vietnam conflict (1964-1975). The Registry is a United States Department of Veterans Affairs (VA) resource that was originally constructed from military records; the Registry has been in existence for almost 20 years. It is one of the largest national twin registries in the US and currently has members living in all 50 states. Initially formed to address questions about the long-term health effects of service in Vietnam, the Registry has evolved into a resource for genetic epidemiological studies of mental and physical health conditions. Several waves of mail and telephone surveys have collected a wealth of health-related information on Registry twins, referred to as members. In addition to twins, selected adult offspring of twins and the mothers of those offspring are also VET Registry members. More recent data collection efforts have focused on specific sets of twin pairs and have conducted detailed clinical or laboratory testing. Selected Vietnam Era Registry Research Studies: * Veteran Health Study * VETSA 2: A Longitudinal Study of Cognitive Aging * Alcoholism Course thought Midlife: A Twin Family Study and Offspring of Twins: G, E and GxE Risk for Alcoholism * GE: Offspring of Twins with Substance Use Disorder * Mechanisms Linking Depression to Cardiovascular Risk (Twins Heart Study 2) * Post-traumatic Stress Disorder and Cardiovascular Disease * Biological Markers for Post-traumatic Stress Disorder (T3) * Memory and the Hippocampus in Vietnam-era Twins with PTSD (Time 3) | twin, male, adult, gene, genetic, post-traumatic stress disorder, cardiovascular disease, child, mother, human, substance-related disorder, depressive disorder, memory, hippocampus, mental health, physical health, epidemiology |
has parent organization: U.S. Department of Veterans Affairs is parent organization of: Vietnam Era Twin Registry Biospecimen Repository |
Aging | nlx_144388 | SCR_008807 | 2026-09-12 01:00:32 | 2 | ||||||||
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Mutation and Patient Database Resource Report Resource Website 1+ mentions |
Mutation and Patient Database (RRID:SCR_018806) | data or information resource, data set, database | Collection of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission. There are two tables for each human NCL disease gene - Patient Datasheets list all published or reported patients and families, and Mutation Datasheets list all published or reported mutations, cross-referenced to patient table. Datasheets are available to view or download as excel files for off-site use to aid local needs or interests. Database follows mutation nomenclature recommendations of Human Genome Variation Society. | Mutation, gene mutation, sequence variations, gene, human NCL disease gene, patient datasheet, mutation datasheet, mutation nomenclature, human genome variation society, data | has parent organization: University College London; London; United Kingdom | Neuronal Ceroid Lipofuscinoses, NCL, Batten disease | Free, Freely available | SCR_018806 | NCL Mutation Database, NCL Mutation and Patient Database | 2026-09-12 12:59:06 | 5 | ||||||||
|
Kaplan Meier Plotter Resource Report Resource Website 1000+ mentions |
Kaplan Meier Plotter (RRID:SCR_018753) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool for meta analysis based discovery and validation of survival biomarkers. Assesses effect of genes on survival using cancer samples including breast, ovarian, lung, and gastric cancer. Sources for databases include GEO, EGA, and TCGA. | Meta analysis, discovery, validation, survival biomarker, gene effect assess, cancer sample, cancer survival gene, gene, cancer, survival, FASEB list | Free, Freely available | SCR_018753 | Kaplan-Meier Plotter, KM plotter | 2026-09-12 12:59:05 | 1816 | ||||||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-09-12 12:59:08 | 4 | ||||||
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Gene Skyline Resource Report Resource Website 10+ mentions |
Gene Skyline (RRID:SCR_019014) | data access protocol, data or information resource, software resource, web service | Browser for general overview of expression profiles for RNA-seq data. Presents expression profiles of selected gene in chosen group of cell types, in either microarray or ULI RNA-seq data. | Expression profiles overwiev, RNAseq data, gene, microarray data, ULI RNAseq data, Immunological Genome Project | Free, Freely available | SCR_019014 | 2026-09-12 12:59:08 | 37 | |||||||||||
|
Cell Ranger Resource Report Resource Website 500+ mentions |
Cell Ranger (RRID:SCR_017344) | data analysis software, data processing software, software application, software resource | Software tool as set of analysis pipelines that process chromium single cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis by 10xGenomics. | Analysis, process, chromium, singe, cell, RNA-seq, align, read, barcode, matrice, clustering, gene, expression, 10xGenomics |
is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology works with: Loupe Browser |
Restricted | SCR_017344 | 2026-09-12 12:58:51 | 722 | ||||||||||
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PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. | Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
NHGRI HG005998; NIGMS P50 GM071508; NIGMS R01 GM071966 |
PMID:25431329 | Free, Freely available | SCR_017353 | 2026-09-12 12:58:52 | 8 | ||||||||
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clusterExperiment Resource Report Resource Website |
clusterExperiment (RRID:SCR_017439) | data analysis software, data processing software, data visualization software, software application, software resource | Software open source R package for executing, evaluating and visualizing different clusterings of experimental data, including data from single cell RNA-Seq studies. Software for running and comparing different clusterings of single cell sequencing data. | Executing, evaluating, visualizing, clustering, experimental, data, single, cell, RNAseq, sequencing, gene, expression, BRAIN Initiative | is recommended by: BRAIN Initiative | Chan Zuckerberg Initiative ; ENS-CFM Data Science Chair ; NIMH U01 MH105979; NIMH U19 MH114830 |
PMID:30180157 | Free, Available for download, Freely available | SCR_017439 | 2026-09-12 12:58:53 | 0 | ||||||||
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HmtPhenome Resource Report Resource Website |
HmtPhenome (RRID:SCR_017289) | data or information resource, data processing software, data visualization software, database, network graph visualization software, service resource, software application, software resource | Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality. Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities. | mitochondria, variant, gene, function, phenotype, data |
uses: Human Phenotype Ontology uses: Ensembl uses: OMIM uses: Orphanet uses: DisGeNET has parent organization: University of Bari; Bari; Italy |
DOI:10.1101/660282 | Free, Freely available | SCR_017289 | 2026-09-12 12:58:51 | 0 | |||||||||
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Scfind Resource Report Resource Website 1+ mentions |
Scfind (RRID:SCR_017339) | data or information resource, data processing software, software application, software resource | Software R package as search tool for single cell RNA-seq data by gene lists. Builds index from scRNA-seq datasets which organizes information in suitable and compact manner so that datasets can be very efficiently searched for either cells or cell types in which given list of genes is expressed. | Single, cell, RNA-seq, data, gene, list, build, index, organize |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | https://genat.uk/post/scfind/, http://bioconductor.org/packages/scfind/, https://github.com/hemberg-lab/scfind | SCR_017339 | 2026-09-12 12:58:51 | 1 | |||||||||
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Glimma Resource Report Resource Website 10+ mentions |
Glimma (RRID:SCR_017389) | data analysis software, data processing software, data visualization software, software application, software resource | Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data. | Interactive, graphic, gene, expression, analysis, visualisation, RNAseq, data |
uses: LIMMA uses: edgeR uses: DESeq2 |
NHMRC ; Victorian State Government Operational Infrastructure Support and Australian Government ; Viertel Fellowship |
PMID:28203714 | Free, Available for download, Freely available | SCR_017389 | 2026-09-12 12:58:52 | 23 | ||||||||
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Functional Annotation Resource Report Resource Website 1+ mentions |
Functional Annotation (RRID:SCR_017519) | service resource | MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO). | MGI, GO, functional, annotation, mouse, gene, product, Gene Ontology |
uses: Gene Ontology has parent organization: Mouse Genome Informatics (MGI) |
Free, Freely available | SCR_017519 | 2026-09-12 12:58:53 | 4 | ||||||||||
|
4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | data or information resource, data repository, database, service resource, storage service resource | Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community. | Repository, chromatic, interaction, data, genomic, region, gene, name, detection, technology, curated | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | r3d100012282 | https://doi.org/10.17616/R3SH37 | SCR_017489 | 2026-09-12 12:58:53 | 11 | ||||||||
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GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | data analysis software, data processing software, software application, software resource | Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. | Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Georgia Institute of Technology; Georgia; USA |
NHGRI HG000783 | PMID:25870408 | Restricted | biotools:GeneMarkS-t | https://bio.tools/GeneMarkS-T | SCR_017648 | 2026-09-12 12:58:55 | 172 | ||||||
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FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. | Two, dimensional, data, reduction, single, cell, RNA seq, visualization, gene, expression, matrix, report, explore, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: University of California at Berkeley; Berkeley; USA |
California Research Alliance by BASF ; National Institutes of Health NRSA Trainee appointment ; NHGRI U01 HG007910; NIMH U01 MH105979 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-09-12 12:58:53 | 0 | ||||||
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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 | 2026-09-12 12:58:54 | 6 | ||||||
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GO Gene Ontology Consortium and Knowledgebase Resource Report Resource Website 10+ mentions |
GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) | GOC | consortium, data or information resource, organization portal, portal | Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems. | Integrate, resource, model, organism, protein, database, gene, ontology, develope, cellular, system | NHGRI HG002273; NHGRI U24 HG012212 |
SCR_017505 | GO Consortium, Gene Ontology Consortium | 2026-09-12 12:58:53 | 10 | |||||||||
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Nomenclature Resource Report Resource Website 1+ mentions |
Nomenclature (RRID:SCR_017511) | data or information resource, service resource | Authoritative source of official names for mouse genes, alleles, and strains. Nomenclature follows rules and guidelines established by International Committee on Standardized Genetic Nomenclature for Mice. | Mouse, gene, allele, strain, rule, guideline, nomenclature | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017511 | 2026-09-12 12:58:53 | 5 | ||||||||||
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Knockout Mouse Project Repository at JAX Resource Report Resource Website |
Knockout Mouse Project Repository at JAX (RRID:SCR_017512) | data or information resource | Information from JAX about their contributions to KOMP project coordinated by International Mouse Phenotyping Consortium. National Institutes of Health has funded three KOMP2 centers in United States, including one at Jackson Laboratory, to work together on task of producing and phenotyping mice to establish resource of knockout mice and related database of gene function. | KOMP, JAX, knockout, mice, data, gene, function, phenotype |
is related to: International Mouse Phenotyping Consortium (IMPC) is related to: JAX Mice and Services has parent organization: Knockout Mouse Project |
Free, Freely available | https://www.jax.org/mouse-search?searchTerm=repository | SCR_017512 | 2026-09-12 12:58:53 | 0 | |||||||||
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Rotor-Gene 6000 series software Resource Report Resource Website 1+ mentions |
Rotor-Gene 6000 series software (RRID:SCR_017552) | data analysis software, data processing software, software application, software resource | Rotor-Gene real-time analysis software system for ROTOR GENE 6000 REAL-TIME PCR machine. Software has been refined to provide an intuitive, Wizard driven interface, enabling flexibility and automation. Build-in extensive analysis, graphing and statistical functions. Unlimited use software license for Windows XP, Pentium IV (2GHz) or higher PC. | Rotor, Gene, 6000 Real Time, PCR machine, analysis, graphing, statistical, function | Free, Available for download, Freely available | https://www.baylor.edu/content/services/document.php/187886.pd | SCR_017552 | Rotor-Gene 6000 series software 1.7 | 2026-09-12 12:58:54 | 3 |
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