Olivier Elemento

Analysis of deep sequencing data	Pathway Analysis
ChIPseeqer: a comprehensive software package for analysis of ChIP-seq data	iPAGE: Information-Theoretic Pathway Analysis of Gene Expression (with H. Goodarzi and Saeed Tavazoie).
Motif discovery
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, coming soon).
Phylogeny
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

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.zip

A 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.

Analysis of deep sequencing data

Pathway Analysis

Motif discovery

Phylogeny

More Software