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  1. hotnet2 hotnet2 Public

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

    Python 101 43

  2. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 86 18

  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 71 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 69 32

  5. GASTON GASTON Public

    Python 40 4

  6. chisel chisel Public

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

    Python 38 11

Repositories

Showing 10 of 92 repositories
  • 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 Mar 5, 2025
  • Multi-GASTON Public
    raphael-group/Multi-GASTON’s past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Mar 3, 2025
  • paste2 Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments v.2

    raphael-group/paste2’s past year of commit activity
    Jupyter Notebook 34 BSD-3-Clause 2 10 0 Updated Mar 2, 2025
  • 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 6 BSD-3-Clause 1 1 0 Updated Feb 28, 2025
  • dialect Public
    raphael-group/dialect’s past year of commit activity
    Python 4 BSD-3-Clause 0 0 0 Updated Feb 27, 2025
  • 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 69 BSD-3-Clause 32 56 5 Updated Feb 26, 2025
  • paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    raphael-group/paste’s past year of commit activity
    Python 86 BSD-3-Clause 18 7 0 Updated Feb 26, 2025
  • MOSAICFlow Public
    raphael-group/MOSAICFlow’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Feb 19, 2025
  • 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 32 BSD-3-Clause 3 3 4 Updated Feb 17, 2025
  • HM-OT Public

    Hidden Markov Optimal Transport: learning the sequence of latent cell-states and transitions in transcriptomic time-series.

    raphael-group/HM-OT’s past year of commit activity
    Python 2 0 0 0 Updated Feb 17, 2025
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