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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 83 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 23

Repositories

Showing 10 of 92 repositories
  • dialect Public
    raphael-group/dialect’s past year of commit activity
    Python 4 BSD-3-Clause 0 0 0 Updated Feb 5, 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 4, 2025
  • dialog Public
    raphael-group/dialog’s past year of commit activity
    0 0 0 0 Updated Feb 4, 2025
  • MOSAICFlow Public
    raphael-group/MOSAICFlow’s past year of commit activity
    Python 0 0 0 0 Updated Feb 3, 2025
  • GASTON-Mix Public
    raphael-group/GASTON-Mix’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Jan 31, 2025
  • GASTON Public
    raphael-group/GASTON’s past year of commit activity
    Python 27 BSD-3-Clause 4 0 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
  • CARTA Public
    raphael-group/CARTA’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated Jan 27, 2025
  • FRLC Public

    Low-rank optimal transport through factor relaxation with latent coupling.

    raphael-group/FRLC’s past year of commit activity
    Jupyter Notebook 4 0 0 0 Updated Jan 24, 2025