Software Packages

biobroom

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

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