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Framework for Metastatic And Clonal History INtegrative Analysis
SPRUCE: Somatic Phylogeny Reconstruction using Combinatorial Enumeration
An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data
HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network
A web application from the Raphael Lab for mutation annotation and genome interpretation.
CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer
A Weighted Exact Test for Mutually Exclusive Mutations in Cancer
Novel Adjacency Identification with Barcoded Reads
Software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.
Raphael group website.
Single species module discovery
Integer Linear Program for the Copy-Number Tree Problem
Tumor Heterogeneity Analysis (THetA) is an algorithm that estimates the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. Please note that the latest release is now called THetA2.
HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.
MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.
A script for converting MAF files for use with MAGI, CoMEt, and HotNet2.
Script for taking the output of the GISTIC2.0 module and converting the data for use with MAGI, HotNet2, and CoMEt.
Docker images for deploying the MAGI web app
A JSON-based statistics server in Tornado for supplying enrichments to MAGI