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Software application for automated power analysis for variance components (VC) quantitative trait locis (QTL) linkage and association tests in sibships, and other common tests (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

A desktop analysis workbench for analyzing high-volume, high-density genotyping data. The software provides a comprehensive set of linkage and association algorithms that allow researchers to discover relationships between genotypes and phenotypes. Researchers can visually explore fully annotated SNPs and genes at varying levels of detail. Designed for biologists and statisticians, GeneSpring GT is capable of importing, visualizing, and analyzing hundreds of thousands of variation measurements simultaneously, for rapid localization of disease or phenotype markers. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

Software application that is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997). (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software application that is a modification of the GENEHUNTER software package (version 1.3)that allows users to perform parametric (LOD-score) analysis of traits caused by imprinted genes - that is, of traits showing a parent-of-origin effect. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software application for multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software application that uses GEE method to estimate the location of the susceptibility gene based on the allele-sharing of affected sib pairs for multiple markers. GENEFINDER can further the analysis of GENEHUNTER by providing a more accurate gene location estimation and the corresponding confidence interval.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for fitting Genetic Epidemiology Models by running stochastic simulation in relation to disease dynamics.

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• SciCrunch
• 14 years ago - by Anonymous

Software application designed to accompany the second edition of Bruce Weir''s book Genetic Data Analysis (1996. Sinauer Associates) (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.

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• SciCrunch
• 14 years ago - by Anonymous

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Software application for statistical analysis of genetic linkage data, sib-pair analysis, association studies (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software package for the management and analysis of pedigree data. it offers: 1. Powerful database management tools, specifically designed for family data; 2. Automatic pedigree drawing; 3. Segregation and linkage analysis, based on traditional maximum likelihood methods and newer, more powerful, Monte Carlo methods that can model both genetic and environmental factors. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Web-based application for testing for locus-locus interaction using genetic association. It is based upon the case-control study design and is designed so that non-specialists may routinely apply tests for interaction. GAIA allows simple testing of both additive and additive plus dominance interaction models and includes permutation testing to appropriately correct for multiple testing. The application is useful for both candidate gene based studies and genome-wide association studies. For large scale studies GAIA includes a screening approach which prioritizes loci for further interaction analysis. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 1st, 2022. Software application for genetic analysis of classical biometric traits like blood pressure or height that are caused by a combination of polygenic inheritance and complex environmental forces. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application for demonstration of method for preliminary ordering of loci based on two-point lod scores. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software application that tests for deviation from Hardy-Weinberg equilibrium and tests for association in case controls studies; Plot genotype frequencies graphically using a de Finetti diagram. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous