# Software Packages

## biobroom

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

## dnamix

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

## edge

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

## eigenR2

This R package calculates a high-dimensional version of the classic $R^2$ statistic.

## 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.

## 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.

## 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.

## 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.

## snm

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

## subSeq

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

## sva

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

## 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.

## trigger

This R package provides tools for the statistical analysis of genetics of gene expression data.