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CENTIPEDE - Inference of Transcription Factor Binding Sites

CENTIPEDE is a method I developed in collaboration with JF Degner, and JK Pritchard that uses PWM information plus experimental data such as DNaseI, histone marks or FAIRE to infer transcription factor binding sites with high specificity [Pubmed]. 

GADA - Genome Alteration Detection Analysis 

GADA is a fast and accurate method for detecting copy number alterations (CNA) and copy number variation (CNV) from array data. It currently exist in two versions:
  • GADA package for R (developed with JR Gonzalez). The latest version can be found [here].
    The associated publication and manual (as supplemental material) can be found here [Pubmed]
    There is also a version available through R-forge (this version may lag behind the one found [here]):
    install.packages("gada", repos="")