Softwares that I developed or co-developed
rSeq - RNA-Seq Analyzer
SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome
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
Glmnet for MATLAB - A matlab wrapper for glmnet, a solver for fitting Lasso (L1) and elastic-net regularized generalized linear models. Algorithm designed by Jerome Friedman, Trevor Hastie and Rob Tibshirani. Fortran code written by Jerome Friedman
Other useful softwares developed by my collaborators
GeneBase - A tool for estimating gene-level expression from Affymetrix exon arrays
MADS - A tool for discovery of differential alternative splicing by exon array
JETTA - Junction and Exon array Toolkit for Transcriptome Analysis
Some small tools that I wrote (email me if you are interested in getting a copy)
bpmapconvert - Convert Affymetrix bpmap files to another version of the genome
bpmaploader - Dump the contents of Affymetrix bpmap files
barloader - Convert between Affymetrix BAR files and text files
draw_figure - Generate different kinds of figures based on different kinds of data, e.g., motif logos for PSSM matrices, heatmaps for Affymetrix CEL files, signal plots for Affymetrix BAR files or text files, etc
License and usage issues
All of the softwares, programs, tools, as well as their source codes and documents (if any), can all be used free of charge for non-commercial usage. For commercial usage, please contact the author. Comments, suggustions, questions, bug reports, etc, are all very welcomed. For all the enquiries, please send to jiangh AT stanford.edu.