# 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
*R*^{2} 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 (~
10^{12} 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