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http://www.seattle.eric.research.va.gov/VETR/Home.asp
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)
Proper citation: Vietnam Era Twin Registry (RRID:SCR_008807) Copy
https://www.ucl.ac.uk/ncl-disease/mutation-and-patient-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of published mutations and sequence variations in genes that cause Neuronal Ceroid Lipofuscinoses together with unpublished data included with permission.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.
Proper citation: Mutation and Patient Database (RRID:SCR_018806) Copy
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.
Proper citation: Kaplan Meier Plotter (RRID:SCR_018753) Copy
http://www.imgt.org/StatClonotype/
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.
Proper citation: IMGT/StatClonotype (RRID:SCR_018963) Copy
http://rstats.immgen.org/Skyline/skyline.html
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.
Proper citation: Gene Skyline (RRID:SCR_019014) Copy
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.
Proper citation: Cell Ranger (RRID:SCR_017344) Copy
http://pathwaynet.princeton.edu/
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.
Proper citation: PathwayNet (RRID:SCR_017353) Copy
https://github.com/epurdom/clusterExperiment
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.
Proper citation: clusterExperiment (RRID:SCR_017439) Copy
https://www.hmtphenome.uniba.it
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.
Proper citation: HmtPhenome (RRID:SCR_017289) Copy
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.
Proper citation: Scfind (RRID:SCR_017339) Copy
https://bioconductor.org/packages/release/bioc/html/Glimma.html
Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.
Proper citation: Glimma (RRID:SCR_017389) Copy
http://www.informatics.jax.org/function.shtml
MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO).
Proper citation: Functional Annotation (RRID:SCR_017519) Copy
https://4dgenome.research.chop.edu/
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.
Proper citation: 4D Genome (RRID:SCR_017489) Copy
http://topaz.gatech.edu/GeneMark/
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.
Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy
https://github.com/YosefLab/FastProject
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.
Proper citation: FastProject (RRID:SCR_017462) Copy
https://amp.pharm.mssm.edu/geneshot/
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.
Proper citation: Geneshot (RRID:SCR_017582) Copy
http://geneontology.org/docs/go-consortium/
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.
Proper citation: GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) Copy
http://www.informatics.jax.org/mgihome/nomen/index.shtml
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.
Proper citation: Nomenclature (RRID:SCR_017511) Copy
https://www.jax.org/research-and-faculty/resources/knockout-mouse-project
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.
Proper citation: Knockout Mouse Project Repository at JAX (RRID:SCR_017512) Copy
http://sydney.edu.au/medicine/bosch/facilities/molecular-biology/nucleic-acid/corbett-rotor-gene.php
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.
Proper citation: Rotor-Gene 6000 series software (RRID:SCR_017552) Copy
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