• Framework for Metastatic And Clonal History INtegrative Analysis

    Jupyter Notebook 4 3 BSD-3-Clause Updated Jul 3, 2018
  • SPRUCE: Somatic Phylogeny Reconstruction using Combinatorial Enumeration

    C++ 7 7 Updated Jun 6, 2018
  • Python 1 2 Updated Jun 5, 2018
  • An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data

    C++ 11 7 Updated Apr 1, 2018
  • HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network

    Python 57 27 Updated Feb 27, 2018
  • Python 2 MIT Updated Feb 16, 2018
  • A web application from the Raphael Lab for mutation annotation and genome interpretation.

    JavaScript 18 7 MIT Updated Feb 16, 2018
  • Python 1 BSD-3-Clause Updated Jan 10, 2018
  • CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

    C 11 12 MIT Updated Jan 4, 2018
  • A Weighted Exact Test for Mutually Exclusive Mutations in Cancer

    Python 5 4 Updated Jan 3, 2018
  • Novel Adjacency Identification with Barcoded Reads

    Python 8 2 Updated Dec 7, 2017
  • Software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.

    C++ 2 1 Updated Dec 5, 2017
  • Raphael group website.

    HTML 1 Updated Nov 8, 2017
  • heinz

    Forked from ls-cwi/heinz

    Single species module discovery

    C++ 3 MIT Updated Nov 1, 2017
  • Integer Linear Program for the Copy-Number Tree Problem

    C++ 1 1 Updated Oct 31, 2017
  • Python 1 4 Updated Aug 11, 2017
  • 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.

    Python 36 18 Updated Jul 31, 2017
  • HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.

    Python 9 5 Updated Jan 16, 2017
  • Javascript library for visualizing genomics data with D3.

    JavaScript 14 2 Updated Jan 6, 2017
  • MultiBreak-SV identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

    Java 6 6 Updated Jul 19, 2016
  • A script for converting MAF files for use with MAGI, CoMEt, and HotNet2.

    Python 2 Updated Jul 11, 2016
  • Script for taking the output of the GISTIC2.0 module and converting the data for use with MAGI, HotNet2, and CoMEt.

    Python 2 Updated Jul 11, 2016
  • Java 1 Updated May 17, 2015
  • Docker images for deploying the MAGI web app

    Shell 1 MIT Updated May 14, 2015
  • A JSON-based statistics server in Tornado for supplying enrichments to MAGI

    Python 1 Updated May 4, 2015
  • Python 6 8 Updated Feb 22, 2015