software
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.
Genetic Heterogeneity: Networks and Pathways
WExT: Weighted Exclusivity Test
WExT computes a statistical score for mutually exclusive mutations using per gene, per sample weights.
More information Download (GitHub) Reference Google Group
CoMEt: Combinations of Exclusive Alterations
CoMEt identifies combinations of exclusive mutations de novo using a statistical score for exclusivity.
More information Download (GitHub) Reference Google Group
HotNet2: Network Analysis of Mutation Data
HotNet2 is an algorithm for the discovery of significantly mutated subnetworks in a protein-protein interaction network.
More information Download (GitHub) Reference Google Group
Multi-Dendrix: (Multiple Pathway De novo Driver Exclusivity)
Multi-Dendrix is an algorithm for the simultaneous discovery of multiple driver pathways using only somatic mutation data from a cohort of samples.
More information Download (GitHub) Reference Google Group
Dendrix: De novo Driver Exclusivity
Dendrix is an algorithm for discovery of mutated driver pathways in cancer using only mutation data.
More information Download (ZIP) Reference Web server
HotNet: Finding Altered Subnetworks
HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.
More information Download (GitHub) Reference Google Group
Structural Variation and Genome Analysis
CNT-MD: Copy-Number Tree Mixture Deconvolution
Software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.
More information Download (GitHub)
CNT-ILP: Copy-Number Tree
Software for inferring the copy-number tree of minimum cost from the copy-number profiles of distinct tumor clones.
More information Download (GitHub)
NAIBR: Novel Adjacency Identification with Barcoded Reads
Software for the identification of novel adjacencies from linked-read whole genome sequencing data.
More information Download (GitHub)
PASTRI: Probabilistic Algorithm for Somatic Tree Inference
Software for inferring the clonal evolution of single-nucleotide given multi-sample tumor sequencing data.
More information Download (GitHub)
SPRUCE: Somatic Phylogeny Reconstruction using Combinatorial Enumeration
Software for inferring the clonal evolution of single-nucleotide and copy-number variants given multi-sample tumor sequencing data.
More information Download (GitHub) Google Group
AncesTree
Software for inferring the clonal evolution of single-nucleotide variants given multi-sample tumor sequencing data.
More information Download (GitHub) Google Group
NAHR Finder
Software for identifying non-allelic homologous recombinations.
MultiBreak-SV
Software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
More information Download (GitHub) Reference
RAIG: Recurrent Aberrations from Interval Graph
RAIG is an algorithm for identifying recurrent and independent copy number aberrations.
More information Download (TAR) Reference
rec-BTP
rec-BTP is a recursive algorithm for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
More information Download (TAR) Reference
THetA: Tumor Heterogeneity Analysis
This algorithm estimates tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.
More information Download (GitHub) Reference Google Group
PREGO: Paired-End Reconstruction of Genome Organization
This algorithm reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired end sequencing data.
More information Download (TAR) Reference
GASVPro: Geometric Analysis of Structural Variants
GASVPro is a probabilistic version of our original GASV algorithm.
More information Download (Google Code) Reference
GASV: Geometric Analysis of Structural Variants
Software for analysis of structural variation from paired-end sequencing and/or array-CGH data
More information Download (Google Code) Reference
NBC: Neighborhood Breakpoint Conservation
This software finds recurrent rearrangement breakpoints in DNA copy number data.
More information Download (TAR) Reference
Gremlin: Genome Rearrangement Explorer with Multi-Scale, Linked Interactions
Gremlin is an interactive visualization model for the comparative analysis of structural variation in human and cancer genomes.
More information Download (Coming Soon) Reference
Additional software
TADtree
TADtree is an algorithm the identification of hierarchical topological domains in Hi-C data.
More information Download (ZIPs)
MAGI: Mutation Annotation & Genome Interpretation
MAGI is a publicly available web application to explore and annotate cancer genomics data.
ExaLT: Accurate Genome-Wide Survival Analysis
ExaLT is an algorithm to compute a rigorous approximation to the log-rank p-value that avoids false discoveries compared to standard tools.
More information Download (ZIPs) Reference
MoDL: Motif Description Length
MoDL finds mutliple motifs in a set of phosphorylated peptides.
More information Download (TAR) Reference