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  • netmix

    NetMix is an algorithm for finding altered subnetworks.

    Python BSD-3-Clause 0 4 0 0 Updated Apr 4, 2020
  • calder

    CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk DNA sequencing data

    Java BSD-3-Clause 0 7 0 0 Updated Apr 2, 2020
  • raphael-group.github.io

    Raphael group website.

    HTML 2 0 0 0 Updated Mar 31, 2020
  • WCND

    Weighted Copy Number Distance

    Python BSD-3-Clause 0 0 0 0 Updated Mar 27, 2020
  • SBMClone

    SBMClone, a method for recovering clonal composition from sparse single-cell mutation data

    Python BSD-3-Clause 0 0 0 0 Updated Mar 19, 2020
  • RCK

    RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes

    Python MIT 0 2 0 0 Updated Mar 11, 2020
  • chisel

    CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links

    Python BSD-3-Clause 1 6 6 0 Updated Feb 11, 2020
  • scarlet

    SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.

    Limbo BSD-3-Clause 0 0 0 0 Updated Jan 8, 2020
  • netNMF-sc

    netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

    Jupyter Notebook BSD-3-Clause 3 10 0 0 Updated Jan 7, 2020
  • hatchet-paper

    Related to (Zaccaria and Raphael, 2018), the repository contains the simulated data, the results of all methods involved in the comparison, the results of HATCHet on the prostate and pancreas cancer datasets, and all data and analysis related to these last two cancer datasets.

    Python 0 1 0 0 Updated Jan 3, 2020
  • hatchet

    HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm 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 4 11 3 0 Updated Oct 4, 2019
  • hierarchical-hotnet

    Hierarchical HotNet is an algorithm for finding hierarchies of active subnetworks.

    Python 9 11 0 2 Updated Oct 2, 2019
  • NAIBR

    Novel Adjacency Identification with Barcoded Reads

    Python MIT 4 9 12 1 Updated Oct 1, 2019
  • decifer

    Copy-aware clustering of somatic single nucleotide variants by the descendant cell fraction

    C++ BSD-3-Clause 1 10 0 0 Updated Sep 12, 2019
  • chisel-data

    CHISEL-DATA -- This is a preliminary repository

    BSD-3-Clause 0 1 0 0 Updated Sep 4, 2019
  • Python 0 1 0 0 Updated Aug 27, 2019
  • Python 5 3 2 0 Updated Aug 16, 2019
  • mascote

    MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution) is a simulation framework to generate sequencing reads with appropriately corrections for the differences in genome lengths between the normal and tumor clone(s) present in multiple mixed samples.

    Python 1 2 0 0 Updated Mar 20, 2019
  • Jupyter Notebook BSD-3-Clause 6 17 4 0 Updated Jan 29, 2019
  • hotnet2

    HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network

    Python 37 70 6 2 Updated Jan 21, 2019
  • hotnet

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

    Python 5 9 0 1 Updated Jan 21, 2019
  • comet

    CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

    C MIT 15 17 9 1 Updated Jan 21, 2019
  • test

    Test private-public

    0 0 0 0 Updated Dec 11, 2018
  • CNT-MD

    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++ 1 4 1 0 Updated Dec 3, 2018
  • wext

    A Weighted Exact Test for Mutually Exclusive Mutations in Cancer

    Python 6 16 8 1 Updated Sep 30, 2018
  • Python 2 1 3 1 Updated Aug 30, 2018
  • spruce

    SPRUCE: Somatic Phylogeny Reconstruction using Combinatorial Enumeration

    C++ 8 11 5 0 Updated Jun 6, 2018
  • AncesTree

    An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data

    C++ 6 13 0 0 Updated Apr 1, 2018
  • Python 0 0 0 0 Updated Mar 24, 2018
  • Python MIT 1 0 0 0 Updated Feb 16, 2018
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