• a new algorithm, Holistic Allele-specific Tumor Copy-number Heterogeneity (HATCHet), that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

    Python 2 1 Updated Dec 18, 2018
  • Framework for Metastatic And Clonal History INtegrative Analysis

    Jupyter Notebook 10 4 BSD-3-Clause Updated Dec 18, 2018
  • Test private-public

    Updated Dec 10, 2018
  • 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++ 5 1 Updated Dec 3, 2018
  • Copy-aware clustering of somatic single nucleotide variants by the descendant cell fraction

    C++ 1 BSD-3-Clause Updated Nov 17, 2018
  • NetMix is an algorithm for finding altered subnetworks.

    Python 2 BSD-3-Clause Updated Nov 15, 2018
  • CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk DNA sequencing data

    Java BSD-3-Clause Updated Nov 8, 2018
  • netNMF: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

    Python BSD-3-Clause Updated Nov 6, 2018
  • Hierarchical HotNet is an algorithm for finding hierarchies of active subnetworks.

    Python 2 1 Updated Oct 2, 2018
  • HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network

    Python 60 29 Updated Sep 30, 2018
  • A Weighted Exact Test for Mutually Exclusive Mutations in Cancer

    Python 8 5 Updated Sep 30, 2018
  • Python 1 2 Updated Aug 30, 2018
  • HotNet is an algorithm for finding significantly altered subnetworks in a large gene interaction network.

    Python 9 5 Updated Aug 17, 2018
  • Novel Adjacency Identification with Barcoded Reads

    Python 8 3 Updated Aug 8, 2018
  • SPRUCE: Somatic Phylogeny Reconstruction using Combinatorial Enumeration

    C++ 7 8 Updated Jun 6, 2018
  • An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data

    C++ 11 7 Updated Apr 1, 2018
  • Python Updated Mar 24, 2018
  • Python 2 MIT Updated Feb 16, 2018
  • A web application from the Raphael Lab for mutation annotation and genome interpretation.

    JavaScript 19 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 13 13 MIT Updated Jan 4, 2018
  • 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++ 2 1 Updated Oct 31, 2017
  • Python 1 4 Updated Aug 11, 2017
  • Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.

    Python 44 20 Updated Jul 31, 2017
  • Javascript library for visualizing genomics data with D3.

    JavaScript 15 3 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