GWASTools - Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

Last updated 15 days ago

snpgeneticvariabilityqualitycontrolmicroarray

10.67 score 17 stars 5 dependents 396 scripts 1.2k downloads

GENESIS - GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.

Last updated 2 months ago

snpgeneticvariabilitygeneticsstatisticalmethoddimensionreductionprincipalcomponentgenomewideassociationqualitycontrolbiocviews

10.36 score 37 stars 1 dependents 342 scripts 646 downloads

SeqVarTools - Tools for variant data

An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.

Last updated 5 months ago

snpgeneticvariabilitysequencinggenetics

8.76 score 3 stars 2 dependents 384 scripts 814 downloads

GWASExactHW - Exact Hardy-Weinburg Testing for Genome Wide Association Studies

Exact Hardy-Weinburg testing (using Fisher's test) for SNP genotypes as typically obtained in a Genome Wide Association Study (GWAS).

Last updated 1 years ago

3.32 score 7 dependents 2 scripts 935 downloads