Analysis of ChIP-seq data |
Pathway Analysis |
 ChIPseeqer: a comprehensive framework for the analysis of ChIP-seq data. |
 iPAGE: Information-Theoretic Pathway Analysis of Gene Expression (with H. Goodarzi and Saeed Tavazoie). |
Motif discovery |
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 FIRE: a universal framework for DNA and RNA motif discovery from expression data. |
 Fastcompare: whole-genome, alignment-free identification of conserved DNA and RNA motifs |
 FIRE-pro: protein motif discovery using mutual information (with D. Lieber and S. Tavazoie). |
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Phylogeny |
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 DTscore / DTdraw : tandem gene duplication tree reconstruction and display |
 IMGT/PhyloGene : online creation of phylogenetic trees for immunoglobulin (IG) and T-cell receptor (TR) genes |
More Software
C implementation of Iclust (Slonim et al, 2005, PNAS): Iclust.tar.gz (code provided by Noam Slonim) MI_MOTIF_DEP.zip (a C program) calculates the mutual information and associated statistical significance between columns of a motif alignment (collection of sites in AlignACE format). A reimplementation in C of CompareACE (for comparing weight matrices) : COMPAREACE.zipA reimplementation of ScanACE (for finding motif weight matrix matches), plus a script to sample sites from weight matrices : MYSCANACE.zip An email-based web page monitoring script (I got very tired of checking up the same rarely-changing pages over and over): WEBMONITOR.zip
Kohonen / Self-Organizing Map (SOM) clustering program (in C): KOHONEN.zip
A C implementation of Dijkstra's shortest paths in a graph (Bellman-Ford algorithm in fact): DIJKSTRA.zip
A very simple and flexible backup script based on rsync
A script for drawing motif maps (like this one): MOTIFMAPS.zip
A Perl module (interfacing some C code) for calculating hypergeometric p-values Hypergeom-0.01.tar
A simple Perl implementation of Cancer Outlier Profile Analysis (COPA), described in Tomlins et al, 2005: COPA.