software

Genetic Heterogeneity: Networks and Pathways

CoMEt: Combinations of Exclusive Alterations

CoMEt identifies combinations of exclusive mutations de novo using a statistical score for exclusivity.

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HotNet2: Network Analysis of Mutation Data

HotNet2 is an algorithm for the discovery of significantly mutated subnetworks in a protein-protein interaction network.

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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.

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Dendrix: De novo Driver Exclusivity

Dendrix is an algorithm for discovery of mutated driver pathways in cancer using only mutation data.

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HotNet: Finding Altered Subnetworks

HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.

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Structural Variation and Genome Analysis

AncesTree

Software for inferring the clonal evolution of multi-sample tumor sequence data.

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NAHR Finder

Software for identifying non-allelic homologous recombinations.

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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.

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RAIG: Recurrent Aberrations from Interval Graph

RAIG is an algorithm for identifying recurrent and independent copy number aberrations.

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rec-BTP

rec-BTP is a recursive algorithm for analyzing intra-tumor heterogeneity from high-throughput sequencing data.

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THetA: Tumor Heterogeneity Analysis

This algorithm estimates tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.

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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.

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GASVPro: Geometric Analysis of Structural Variants

GASVPro is a probabilistic version of our original GASV algorithm.

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GASV: Geometric Analysis of Structural Variants

Software for analysis of structural variation from paired-end sequencing and/or array-CGH data

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NBC: Neighborhood Breakpoint Conservation

This software finds recurrent rearrangement breakpoints in DNA copy number data.

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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.

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Additional software

TADtree

TADtree is an algorithm the identification of hierarchical topological domains in Hi-C data.

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MAGI: Mutation Annotation & Genome Interpretation

MAGI is a publicly available web application to explore and annotate cancer genomics data.

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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.

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MoDL: Motif Description Length

MoDL finds mutliple motifs in a set of phosphorylated peptides.

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