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http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application to compute composite measures of linkage disequilibrium, their variances and covariances, and statistical tests, for all pairs of alleles from two loci when linkage phase is unkown. An extension of Weir and Cockerham (1989) to apply to multi-allelic loci. (entry from Genetic Analysis Software)

Proper citation: COMPOSITELD (RRID:SCR_013132) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/eathomp/Anonftp/PANGAEA/BOREL/

Software application for inference of genealogical relationships from genetic data, including sibship inference.

Proper citation: BOREL (RRID:SCR_013135) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application for statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms. (entry from Genetic Analysis Software)

Proper citation: GASSOC (RRID:SCR_013136) Copy   

•   Source: SciCrunch Registry

http://www.bio.unc.edu/faculty/vision/lab/mappop/

Software application that selects high resolution mapping subsamples and performs bin mapping (entry from Genetic Analysis Software)

Proper citation: MAPPOP (RRID:SCR_013490) Copy   

•   Source: SciCrunch Registry

http://dlin.web.unc.edu/software/SNPMStat/

A command-line program for the statistical analysis of SNP-disease association in case-control/cohort/cross-sectional studies with potentially missing genotype data. SNPMStat allows the user to estimate or test SNP effects and SNP-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty, study design and gene-environment dependence. For SNPs without missing data, the program performs the standard association analysis. For typed SNPs with missing data or untyped SNPs, the program performs the maximum-likelihood analysis. (entry from Genetic Analysis Software)

Proper citation: SNPMSTAT (RRID:SCR_013339) Copy   

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http://www.cbil.ece.vt.edu/ResearchOngoingSNP.htm

Software application (entry from Genetic Analysis Software)

Proper citation: MECPM (RRID:SCR_013341) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/MAOS/

Software application that implements valid and efficient statistical methods for meta-analysis of genomewide association studies with overlapping subjects. The current release performs logistic regression analysis of individual level data under the additive mode of inheritance. Data from genome-wide association studies are often analyzed jointly for the purposes of combining information from multiple studies of the same disease or comparing results across different disorders. In many instances, the same subjects appear in multiple studies. Failure to account for overlapping subjects can greatly inflate type I error when combining results from multiple studies of the same disease and can drastically reduce power when comparing results across different disorders. (entry from Genetic Analysis Software)

Proper citation: MAOS (RRID:SCR_013351) Copy   

•   Source: SciCrunch Registry

http://mmrrc.ucdavis.edu/

Center that imports, archives, maintains, and distributes mutant mouse alleles as live mice, frozen germplasm, stem cells, and molecular vectors for use in biomedical research. The MMRRC Davis receives transgenics, knockouts, and other kinds of mutant mouse lines at no cost to the donor, and after re-derivation and cryopreservation, distributes breeding stock, germplasm, cells, or tissues of genetically-defined and pathogen-free mice for a small fee to requesting investigators.

Proper citation: University of California at Davis Mutant Mouse Resource and Research Center (RRID:SCR_016448) Copy   

•   Source: SciCrunch Registry

http://www.mmrrc.missouri.edu/

Center that supplies mice and conducts research projects focused on the role of mice as animal models. Some of these projects include refinement of models to ensure study reproducibility, as well as development and improvement of economical methods for cryopreservation of mouse strains.

Proper citation: Mutant Mouse Resource and Research Center - University of Missouri (RRID:SCR_016447) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/ReBATE

Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .

Proper citation: ReBATE (RRID:SCR_017139) Copy   

•   Source: SciCrunch Registry

http://www.vet.upenn.edu/research/core-resources-facilities/referral-center-for-animal-models

Center that aims to discover, characterize, maintain breeding colonies, and make available dog and cat models with hereditary diseases homologous to those found in human patients that can be used to translate preclinical trials from kennel to clinic. The animal models represent true orthologs of their respective human disease, involving defects in homologous genes resulting in similar molecular, biochemical, pathological, and clinical phenotype as in human patients.

Proper citation: Referral Center for Animal Models of Human Genetic Diseases (RRID:SCR_016453) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~junzhang/LAPSTRUCT.html

Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software)

Proper citation: LAPSTRUCT (RRID:SCR_007550) Copy   

•   Source: SciCrunch Registry

http://www.alspac.bris.ac.uk

A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.

Proper citation: ALSPAC (RRID:SCR_007260) Copy   

•   Source: SciCrunch Registry

http://www.pedigree-draw.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software)

Proper citation: Pedigree-Draw (RRID:SCR_008302) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/ccle/

A collaborative project between the Broad Institute and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation, with the goal of conducting a detailed genetic and pharmacologic characterization of a large panel of human cancer models. The CCLE also works to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

Proper citation: Cancer Cell Line Encyclopedia (RRID:SCR_013836) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ibdreg/index.html

Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software)

Proper citation: IBDREG (RRID:SCR_013127) Copy   

•   Source: SciCrunch Registry

https://www.ars-grin.gov/npgs/

Cooperative effort by U.S. state and federal government and private organizations to preserve the genetic diversity of plants. The NPGS aids scientists and the need for genetic diversity by acquiring, preserving, evaluating, documenting and distributing crop germplasm. The NPGS is managed by the Agricultural Research Service (ARS), the in-house research agency of the United States Department of Agriculture (USDA). Funding for the NPGS comes primarily through appropriations from the U.S. Congress.

Proper citation: National Plant Germplasm System (NPGS) (RRID:SCR_016785) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/

Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.

Proper citation: BASTA (RRID:SCR_017303) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn4921369/wiki/235539

Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.

Proper citation: PsychENCODE Knowledge Portal (RRID:SCR_017500) Copy   

•   Source: SciCrunch Registry

http://magest.hgc.jp/

A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future.

Proper citation: MAboya Gene Expression Patterns and Sequence Tags (RRID:SCR_000763) Copy   

•   Source: SciCrunch Registry