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  1. hotnet2 hotnet2 Public

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

    Python 100 43

  2. paste paste Public

    Probabilistic Alignment of Spatial Transcriptomics Experiments

    Python 84 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. 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 24

Repositories

Showing 10 of 92 repositories
  • MOSAICFlow Public
    raphael-group/MOSAICFlow’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Feb 19, 2025
  • dialect Public
    raphael-group/dialect’s past year of commit activity
    Python 4 BSD-3-Clause 0 0 0 Updated Feb 17, 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 30 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
  • DeST_OT Public

    Developmental Spatiotemporal Optimal Transport

    raphael-group/DeST_OT’s past year of commit activity
    Jupyter Notebook 8 BSD-3-Clause 1 0 0 Updated Feb 12, 2025
  • dialog Public
    raphael-group/dialog’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Feb 8, 2025
  • GASTON-Mix Public
    raphael-group/GASTON-Mix’s past year of commit activity
    Python 2 BSD-3-Clause 0 0 0 Updated Feb 7, 2025
  • GASTON Public
    raphael-group/GASTON’s past year of commit activity
    Python 31 BSD-3-Clause 4 1 0 Updated Jan 31, 2025
  • raphael-group/spatial_anomaly_detection’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Jan 30, 2025
  • startle Public

    cellular lineage reconstruction from lineage tracing data

    raphael-group/startle’s past year of commit activity
    C++ 4 MIT 2 0 0 Updated Jan 29, 2025