Gene Expression

rSeqNP - A non-parametric approach for detecting differential expression and splicing from RNA-Seq data

rSeqDiff - Detecting differential isoform expression from RNA-seq data

rSeq - RNA-Seq Analyzer

mseq - An R package for modeling non-uniformity in short-read rates in RNA-Seq data

Read Alignment

SpliceMap - Splice Junction Discovery Using RNA-Seq

SeqAlto - Fast and Accurate Read Alignment for Resequencing

SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome

Density Estimation

fast-opt - Package for fast computation of the Optional Polya Tree

smooth-opt - Smoothing the OPT partition

Genomic Data Visualization

CisGenome Browser - A Compact Stand-Alone Genome Browser

CisGenome - An integrated tool for tiling array, genome and cis-regulatory element analysis, working together with CisGenome Browser

Penalized Regression

Glmnet for MATLAB - A matlab wrapper for glmnet, a solver for fitting Lasso (L1) and elastic-net regularized generalized linear models.