Dendrix (De novo Driver Exclusivity) is an algorithm for discovery of mutated driver pathways in cancer using only mutation data. It finds sets of genes, domains, or nucleotides whose mutations exhibit both high coverage and high exclusivity in the analyzed samples.
Zodiac is a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.”
PINCAGE is a method that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450K array DNA methylation measurements of promoters as well as gene bodies.
HMCan is Hidden Markov Model based tool that is developed to detect histone modification in cancer ChIP-seq data. It applies three correction steps to the data: copy number correction, GC bias correction and noise level correction.
HMCan-diff is a method designed specially to detect changes of histone modifications in ChIP-seq cancer samples or between a cancer sample and a normal control. HMCan-diff explicitly corrects for copy number bias as well as for other ChIP-seq technical biases such as GC-content and mappability biases, and variable levels of signal-to-noise in different samples. HMCan-diff uses a three state hidden Markov model to detect regions of differential histone modifications.