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https://github.com/Kingsford-Group/kourami
Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.
Proper citation: Kourami (RRID:SCR_022280) Copy
https://gillisweb.cshl.edu/Primate_MTG_coexp/
We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain.
Proper citation: Gene functional conservation across cell types and species (RRID:SCR_023292) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This website contains a database of the mouse SNP. DNA sequencing was performed along with genotyping. There is information on genotyping, mouse strain, and haplotype map.
Proper citation: Mouse Single Nucleotide Polymorphism Database (RRID:SCR_000033) Copy
Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs.
Proper citation: International Knockout Mouse Consortium (RRID:SCR_005574) Copy
http://worfdb.dfci.harvard.edu/
Database that integrates and disseminates the data from the cloning of complete set of predicted protein-encoding ORFs of Caenorhabditis elegans. It also allows the community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for ORFs originally predicted by the C. elegans sequencing consortium. The database contains this OST information along with data pertinent to the cloning process.
Proper citation: WorfDB (RRID:SCR_006028) Copy
http://www.informatics.jax.org
International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI.
Proper citation: Mouse Genome Informatics (MGI) (RRID:SCR_006460) Copy
http://research.nhgri.nih.gov/CGD/
Manually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases.
Proper citation: Clinical Genomic Database (RRID:SCR_006427) Copy
http://chgr.mc.vanderbilt.edu/page/gist
Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix.
Proper citation: Genotype-IBD Sharing Test (RRID:SCR_006257) Copy
http://www.sanger.ac.uk/mouseportal/
Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen.
Proper citation: Sanger Mouse Resources Portal (RRID:SCR_006239) Copy
Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.
Proper citation: Bioconductor (RRID:SCR_006442) Copy
http://code.google.com/p/annotare/
A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.
Proper citation: Annotare (RRID:SCR_000319) Copy
Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform.
Proper citation: khmer (RRID:SCR_001156) Copy
http://bioconductor.org/packages/release/bioc/html/nondetects.html
Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.
Proper citation: nondetects (RRID:SCR_001702) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
A custom genome browser which provides detailed answers to questions on the haplotype diversity and phylogenetic origin of the genetic variation underlying any genomic region of most laboratory strains of mice (both classical and wild-derived). Users can select a region of the genome and a set of laboratory strains and/or wild caught mice. The region is selected by specifying the start (e.g. 31200000 or 31200K or 31.2M), and end of the interval and the chromosome (i.e, autosome number and X chromosome). Samples can be selected by name or by entire set. Data sets include information on subspecific origin, heterozygosity regions, and haplotype coloring, among others.
Proper citation: Mouse Phylogeny Viewer (RRID:SCR_014071) Copy
https://www.clinicalgenome.org
Genomics knowledgebase for clinical relevance of genes and variants for use in research. ClinGen's primary function is to store and share information for the benefit of the scientific community. Laboratory scientists, clinicians, and patients can share and access data.
Proper citation: ClinGen (RRID:SCR_014968) Copy
https://vertebrate.genenames.org/
Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.
Proper citation: VGNC (RRID:SCR_017514) Copy
Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome.
Proper citation: SRMAtlas (RRID:SCR_016996) Copy
https://gitlab.com/rosen-lab/white-adipose-atlas
Single cell atlas of human and mouse white adipose tissue.
Proper citation: White Adipose Atlas (RRID:SCR_023625) Copy
Open database of polygenic scores and relevant metadata required for accurate application and evaluation. Used for reproducibility and systematic evaluation.
Proper citation: Polygenic Score Catalog (RRID:SCR_023558) Copy
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