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Popular repositories

  1. hotnet2 Public

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

    Python 87 45

  2. THetA Public

    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 re…

    Python 65 31

  3. hatchet Public

    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, a…

    Roff 37 19

  4. paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 34 10

  5. chisel Public

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

    Python 30 8

  6. machina Public

    Framework for Metastatic And Clonal History INtegrative Analysis

    Jupyter Notebook 28 11

Repositories

  • hatchet Public

    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.

    Roff 37 BSD-3-Clause 19 11 3 Updated Jun 30, 2022
  • belayer Public
    Jupyter Notebook 1 0 0 0 Updated Jun 27, 2022
  • decifer Public

    DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).

    Jupyter Notebook 12 BSD-3-Clause 4 6 0 Updated Jun 20, 2022
  • raphael-group.github.io Public

    Raphael group website.

    HTML 0 2 0 0 Updated May 18, 2022
  • paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 34 BSD-3-Clause 10 1 0 Updated May 18, 2022
  • Jupyter Notebook 3 0 0 0 Updated May 18, 2022
  • MICRO Public
    Python 0 0 0 0 Updated May 15, 2022
  • chisel Public

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

    Python 30 BSD-3-Clause 8 0 1 Updated Apr 30, 2022
  • STARCH Public

    Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity

    Python 9 MIT 7 7 1 Updated Apr 25, 2022
  • NAIBR Public

    Novel Adjacency Identification with Barcoded Reads

    Python 12 MIT 5 14 4 Updated Apr 19, 2022

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