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  1. hotnet2 hotnet2 Public

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

    Python 98 43

  2. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 73 17

  3. THetA 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 70 33

  4. hatchet 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 62 30

  5. chisel chisel Public

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

    Python 37 11

  6. hierarchical-hotnet hierarchical-hotnet Public

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

    Python 36 23

Repositories

Showing 10 of 80 repositories
  • CalicoST Public

    Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

    raphael-group/CalicoST’s past year of commit activity
    Python 5 BSD-3-Clause 2 0 1 Updated Jul 3, 2024
  • fastBE Public
    raphael-group/fastBE’s past year of commit activity
    Jupyter Notebook 5 0 0 0 Updated Jul 2, 2024
  • LAML Public

    LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data

    raphael-group/LAML’s past year of commit activity
    Python 2 GPL-3.0 0 0 0 Updated Jun 25, 2024
  • 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.

    raphael-group/hatchet’s past year of commit activity
    Roff 62 BSD-3-Clause 30 50 4 Updated Jun 25, 2024
  • GASTON Public
    raphael-group/GASTON’s past year of commit activity
    Python 13 BSD-3-Clause 2 3 0 Updated Jun 24, 2024
  • DeST_OT Public

    Developmental Spatiotemporal Optimal Transport

    raphael-group/DeST_OT’s past year of commit activity
    Jupyter Notebook 4 BSD-3-Clause 1 0 0 Updated Jun 8, 2024
  • startle Public
    raphael-group/startle’s past year of commit activity
    C++ 4 MIT 1 0 0 Updated Jun 4, 2024
  • dialect Public
    raphael-group/dialect’s past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated May 21, 2024
  • decifer Public

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

    raphael-group/decifer’s past year of commit activity
    Jupyter Notebook 19 BSD-3-Clause 7 8 0 Updated May 21, 2024
  • laml-experiments Public

    experiments for the LAML paper

    raphael-group/laml-experiments’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated May 16, 2024
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