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  1. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 106 22

  2. hotnet2 hotnet2 Public

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

    Python 102 43

  3. GASTON GASTON Public

    GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data

    Python 77 16

  4. 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 76 29

  5. 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 73 34

  6. CalicoST CalicoST Public

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

    Python 52 4

Repositories

Showing 10 of 103 repositories
  • cnplot Public

    A dedicated plotting library for copy numbers

    raphael-group/cnplot's past year of commit activity
    Python 0 MIT 0 0 0 Updated Nov 12, 2026
  • phyloGMM Public

    a phylogenetic mixture model for simultaneous inference of cell types and transitions from single-cell lineage tracing data

    raphael-group/phyloGMM's past year of commit activity
    C++ 0 0 0 0 Updated Nov 7, 2026
  • SUMMIT Public

    SUMMIT: Scalable Unified Metastatic Migration Inference on Trees

    raphael-group/SUMMIT's past year of commit activity
    Python 0 0 0 0 Updated Nov 6, 2026
  • troupe Public

    Code for Tree-informed Rate Optimization Using Potency Enforcement and associated experiments

    raphael-group/troupe's past year of commit activity
    Python 1 0 0 0 Updated Nov 5, 2026
  • troupe-experiments Public
    raphael-group/troupe-experiments's past year of commit activity
    Python 0 0 0 0 Updated Nov 5, 2026
  • Universal-Genotyping-Pipeline Public
    raphael-group/Universal-Genotyping-Pipeline's past year of commit activity
    Python 0 1 0 0 Updated Oct 30, 2026
  • MGW Public
    raphael-group/MGW's past year of commit activity
    Python 10 3 0 0 Updated Oct 7, 2026
  • 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 73 BSD-3-Clause 34 56 5 Updated Sep 29, 2026
  • dialect Public
    raphael-group/dialect's past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Sep 26, 2026
  • LAML-Pro Public
    raphael-group/LAML-Pro's past year of commit activity
    C++ 4 2 1 1 Updated Aug 6, 2026
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