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    82 repositories

    • 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.
      Roff
      •
      BSD 3-Clause "New" or "Revised" License
      •31•67•55•4•Updated Oct 16, 2024Oct 16, 2024

    • paste3

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•8•2•Updated Oct 16, 2024Oct 16, 2024

    • chimeric-epistasis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 13, 2024Oct 13, 2024

    • fastBE

      Public
      Jupyter Notebook
      •0•5•0•0•Updated Oct 8, 2024Oct 8, 2024

    • LAML

      Public
      LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
      single-cellphylogenymaximum-likelihood-estimationtree-inferencelineage-tracing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Sep 29, 2024Sep 29, 2024

    • lazac-copy-number

      Public
      C++
      •0•5•1•0•Updated Sep 25, 2024Sep 25, 2024

    • DeST_OT

      Public
      Developmental Spatiotemporal Optimal Transport
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•6•0•0•Updated Sep 16, 2024Sep 16, 2024

    • CalicoST

      Public
      Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•9•0•2•Updated Sep 10, 2024Sep 10, 2024

    • MOLLUSC

      Public
      Maximum Likelihood Estimation Of Lineage and Location Using Single Cell Spatial Lineage tracing Data
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • startle

      Public
      C++
      •
      MIT License
      •1•4•0•0•Updated Sep 4, 2024Sep 4, 2024

    • copulacci

      Public
      Jupyter Notebook
      •0•4•1•0•Updated Sep 4, 2024Sep 4, 2024

    • MERLIN

      Public
      Python
      •0•6•2•0•Updated Aug 29, 2024Aug 29, 2024

    • GASTON

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•16•0•0•Updated Aug 29, 2024Aug 29, 2024

    • CARTA

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Aug 21, 2024Aug 21, 2024

    • ConDoR

      Public
      Python
      •
      MIT License
      •1•7•0•1•Updated Aug 21, 2024Aug 21, 2024

    • laml-experiments

      Public
      experiments for the LAML paper
      Jupyter Notebook
      •0•0•0•0•Updated Aug 14, 2024Aug 14, 2024

    • dialect

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Aug 5, 2024Aug 5, 2024

    • STARCH

      Public
      Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
      Python
      •
      MIT License
      •9•18•10•1•Updated Jul 22, 2024Jul 22, 2024

    • decifer

      Public
      DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•20•8•0•Updated May 21, 2024May 21, 2024

    • hetdetect

      Public
      Inferring Het SNP positions from tumor samples using Hidden Markov Models
      Python
      •1•0•0•0•Updated May 3, 2024May 3, 2024

    • sc-mail-experiments

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 8, 2024Apr 8, 2024

    • hatchet2-simulations

      Public
      Snakemake pipeline for generating and running on new simulated data for HATCHet2 revisions
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 2, 2024Apr 2, 2024

    • hatchet2-paper

      Public
      Publication repository for results that accompany the HATCHet2 paper.
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 2, 2024Apr 2, 2024

    • intmemoir-processed-data

      Public
      0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

    • raphael-group.github.io

      Public
      Raphael group website.
      HTML
      •2•0•0•0•Updated Feb 29, 2024Feb 29, 2024

    • scarlet

      Public
      SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.
      phylogeneticscancer-genomicssingle-celltumor-evolutiontumor-phylogenyalgorithm
      Limbo
      •
      BSD 3-Clause "New" or "Revised" License
      •4•8•2•1•Updated Feb 21, 2024Feb 21, 2024

    • paste2

      Public
      Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•28•6•0•Updated Dec 26, 2023Dec 26, 2023

    • belayer

      Public
      Jupyter Notebook
      •1•5•0•0•Updated Dec 4, 2023Dec 4, 2023

    • calder

      Public
      CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk DNA sequencing data
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •1•15•9•0•Updated Nov 28, 2023Nov 28, 2023

    • chisel

      Public
      CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•38•7•1•Updated Nov 19, 2023Nov 19, 2023