Software

biobroom. This R package converts standard objects constructed by bioinformatics packages, especially those in Bioconductor, to the tidy data format. Bioconductor / GitHub

bnpsd. This R package simulates admixed populations via simulated allele frequencies and genotypes from the BN-PSD (“Balding-Nichols Pritchard-Stephens-Donnelly”) admixture model. This model enables the simulation of complex population structures, ideal for illustrating challenges in kinship coefficient and F_ST estimation. CRAN / GitHub

dnamix. This Fortran program calcluates likelihood ratios as they pertain to mixed DNA samples encountered in forensic science. GitHub

edge. This R package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Bioconductor / GitHub

eigenR2. This R package calculates a high-dimensional version of the classic R² statistic. GitHub

gcatest. This R package implements the genotype-conditional association test (GCATest), which is an association test for genome wide association studies that controls for population structure under a general class of trait models. Bioconductor / GitHub

jackstraw. This R package calculates a ignificance test for association between variables and their estimated latent variables. Latent variables may be estimated by principal component analysis (PCA), logistic factor analysis (LFA), and other techniques. CRAN / GitHub

lfa. This R package implements logistic factor analysis, which is a PCA analogue on Binomial data via estimation of latent structure in the natural parameter space. Bioconductor / GitHub

popkin. The popkin (“population kinship”) R package estimates the kinship matrix of individuals and F_ST from their biallelic genotypes. Our estimation framework is the first to be practically unbiased under arbitrary population structures. CRAN / GitHub

qvalue. This R package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. Bioconductor / GitHub

snm. This R package performs a supervised normalization of microarray data that takes into account the study design. Bioconductor

subSeq. This R package performs subsampling of high throughput sequencing count data for use in experimental design and analysis. Bioconductor / GitHub

sva. This R package performs surrogate variable analysis to account for sources of systematic variation not included in the study design model. Bioconductor / GitHub

terastructure. This C++ program fits the admixture model on tera-sample-sized data sets (~ 10¹² observed genotypes). This package provides a scalable, multi-threaded implementation that can be run on a single computer. GitHub

trigger. This R package provides tools for the statistical analysis of genetics of gene expression data. Bioconductor / GitHub