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CshlSiepelLab

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  1. phast phast Public

    PHAST

    C 83 30

  2. LINSIGHT LINSIGHT Public

    C++ 26 9

  3. arg-selection arg-selection Public

    ARG-based inference of selection using deep learning

    Python 17 3

  4. argweaver argweaver Public

    Forked from mjhubisz/argweaver

    Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

    C++ 14 3

  5. RPHAST RPHAST Public

    RPHAST: Phylogenetic Analysis with Space/Time Models in R

    C 13 4

  6. super-enhancer-code super-enhancer-code Public

    Code for Nature Genetics correspondance, "Is a super-enhancer greater than the sum of its parts?" (2016).

    R 9 2

Repositories

Showing 10 of 27 repositories
  • phast Public

    PHAST

    CshlSiepelLab/phast’s past year of commit activity
    C 83 BSD-3-Clause 30 2 2 Updated Apr 14, 2026
  • vine Public

    Variational Inference with Node Embedding for Bayesian phylogenetics

    CshlSiepelLab/vine’s past year of commit activity
    C 5 1 0 1 Updated Apr 8, 2026
  • graphposterior Public

    Python package to interpret a posterior distribution of cell lineage trees and migration histories, simulate metastatic cancer CRISPR lineage-tracing data, and some other utility functions.

    CshlSiepelLab/graphposterior’s past year of commit activity
    C++ 0 MIT 1 0 0 Updated Apr 8, 2026
  • bioconda-recipes Public Forked from bioconda/bioconda-recipes

    Conda recipes for the bioconda channel.

    CshlSiepelLab/bioconda-recipes’s past year of commit activity
    Shell 0 MIT 3,871 0 0 Updated Mar 13, 2026
  • homebrew-tools Public

    support for homebrew distributions

    CshlSiepelLab/homebrew-tools’s past year of commit activity
    Ruby 0 0 0 0 Updated Mar 13, 2026
  • beam Public

    BEAST2 package to infer cancer migration histories from CRISPR single-cell lineage tracing data.

    CshlSiepelLab/beam’s past year of commit activity
    Java 2 GPL-3.0 0 0 0 Updated Mar 6, 2026
  • beam_experiments Public

    Pipelines and scripts used for analyses in the BEAM method paper.

    CshlSiepelLab/beam_experiments’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Feb 10, 2026
  • staged-recipes Public Forked from conda-forge/staged-recipes

    A place to submit conda recipes before they become fully fledged conda-forge feedstocks

    CshlSiepelLab/staged-recipes’s past year of commit activity
    Python 0 BSD-3-Clause 5,929 0 0 Updated Jan 5, 2026
  • arg_explorer Public

    Repo for running and comparing ARG inference methods

    CshlSiepelLab/arg_explorer’s past year of commit activity
    Python 0 0 0 0 Updated Oct 17, 2025
  • argweaver-d-analysis Public

    Scripts for Hubisz et al 2019 "Mapping gene flow between ancient hominins..."

    CshlSiepelLab/argweaver-d-analysis’s past year of commit activity
    R 8 2 2 0 Updated Sep 29, 2025
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