This page lists some of the software packages developed in the group, organized by topic. For the most up-to-date list of software, please visit the group Github repository.
WExT computes a statistical score for mutually exclusive mutations using per gene, per sample weights.
CoMEt identifies combinations of exclusive mutations de novo using a statistical score for exclusivity.
HotNet2 is an algorithm for the discovery of significantly mutated subnetworks in a protein-protein interaction network.
Multi-Dendrix is an algorithm for the simultaneous discovery of multiple driver pathways using only somatic mutation data from a cohort of samples.
Dendrix is an algorithm for discovery of mutated driver pathways in cancer using only mutation data.
HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.
Software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.
Software for inferring the copy-number tree of minimum cost from the copy-number profiles of distinct tumor clones.
Software for the identification of novel adjacencies from linked-read whole genome sequencing data.
Software for inferring the clonal evolution of single-nucleotide given multi-sample tumor sequencing data.
Software for inferring the clonal evolution of single-nucleotide and copy-number variants given multi-sample tumor sequencing data.
Software for inferring the clonal evolution of single-nucleotide variants given multi-sample tumor sequencing data.
Software for identifying non-allelic homologous recombinations.
Software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
RAIG is an algorithm for identifying recurrent and independent copy number aberrations.
rec-BTP is a recursive algorithm for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
This algorithm estimates tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.
This algorithm reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired end sequencing data.
GASVPro is a probabilistic version of our original GASV algorithm.
Software for analysis of structural variation from paired-end sequencing and/or array-CGH data
This software finds recurrent rearrangement breakpoints in DNA copy number data.
Gremlin is an interactive visualization model for the comparative analysis of structural variation in human and cancer genomes.
TADtree is an algorithm the identification of hierarchical topological domains in Hi-C data.
MAGI is a publicly available web application to explore and annotate cancer genomics data.
ExaLT is an algorithm to compute a rigorous approximation to the log-rank p-value that avoids false discoveries compared to standard tools.
MoDL finds mutliple motifs in a set of phosphorylated peptides.