ClaNC: This software implements new methodology to make classifications based on high-throughput genomic data, such as DNA microarray data. Written by Alan Dabney.
DNAMIX: Calculates likelihood ratios as they pertain to mixed DNA samples encountered in forensic science. Written by John Storey.
eCADS: Software to normalize two-channel microarrays using the new efficient common array dye swap method. eCADS removes intensity-dependent biases, while accounting for the experimental design. Written by Alan Dabney.
EDGE: A comprehensive software package for the significance analysis of DNA microarray experiments -- for both standard and time course experiments -- based on our new optimal discovery procedure and time course methodology. Written by Jeff Leek, Alan Dabney, Eva Monsen, and John Storey.
QVALUE: The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. This software takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. Written by Alan Dabney and John Storey.
SVA: It has been shown that genome-wide expression may be affected by environmental, demographic, genetic and technical factors, creating what we call expression heterogeneity. Surrogate variable analysis (SVA) is designed to identify, estimate, and incorporate into an analysis the sources of expression heterogeneity that are not captured by variables included in the model. SVA has been shown to reduce dependence across genes, stablize false discovery rate estimates, and improve reproducibility of analyses. Written by Jeff Leek and John Storey.