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mccoy-lab

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  1. MAGE MAGE Public

    Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.

    R 42 5

  2. karyohmm karyohmm Public

    Implementation of the karyoHMM model for assessing aneuploidy in PGT data

    Python

  3. LD-PGTA LD-PGTA Public

    Linkage disequlibrium-informed PGT-A (LD-PGTA). A package for detecting genotypic signatures of aneuploidy from extremely low-coverage sequence data.

    Python 18 1

  4. t2t-variants t2t-variants Public

    Code associated with the manuscript "A complete reference genome improves analysis of human genetic variation".

    R 17 3

  5. hgv_modules hgv_modules Public

    Teaching modules for Human Genome Variation Lab.

    R 20 6

  6. rhapsodi rhapsodi Public

    R haploid sperm/oocyte data imputation (rhapsodi). A package for analysis of low-coverage single-cell sequencing data from multiple gametes.

    R 4

Repositories

Showing 10 of 19 repositories
  • 1kgp_chm13_maps Public
    mccoy-lab/1kgp_chm13_maps’s past year of commit activity
    R 2 0 1 0 Updated Jan 12, 2026
  • karyohmm Public

    Implementation of the karyoHMM model for assessing aneuploidy in PGT data

    mccoy-lab/karyohmm’s past year of commit activity
    Python 0 MIT 0 4 (2 issues need help) 1 Updated Dec 25, 2025
  • natera_recomb Public
    mccoy-lab/natera_recomb’s past year of commit activity
    Jupyter Notebook 0 0 2 0 Updated Dec 1, 2025
  • natera_genotyping Public

    Genotyping + imputation workflow for parental data in Natera Spectrum + Anora datasets

    mccoy-lab/natera_genotyping’s past year of commit activity
    Python 0 0 0 0 Updated Oct 24, 2025
  • natera_aneuploidy Public

    GWAS + QuantGen of Aneuploidy in Natera PGT Data

    mccoy-lab/natera_aneuploidy’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 24, 2025
  • aneuploidyRates Public

    A repository code that estimates the meiotic and mitotic aneuploidy rates of an embryo

    mccoy-lab/aneuploidyRates’s past year of commit activity
    R 1 1 0 1 Updated Jul 22, 2025
  • hgv_modules Public

    Teaching modules for Human Genome Variation Lab.

    mccoy-lab/hgv_modules’s past year of commit activity
    R 20 CC-BY-4.0 6 0 1 Updated Jun 6, 2025
  • MAGE Public

    Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.

    mccoy-lab/MAGE’s past year of commit activity
    R 42 5 0 1 Updated Jul 19, 2024
  • LD-CHASE Public

    A tool for linkage disequilibrium-informed comparison of haplotypes among sibling embryos.

    mccoy-lab/LD-CHASE’s past year of commit activity
    Python 4 1 0 0 Updated Oct 13, 2023
  • transmission-distortion Public

    Analysis scripts for "A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel's first law across a large sample of human sperm" https://elifesciences.org/articles/76383

    mccoy-lab/transmission-distortion’s past year of commit activity
    R 1 0 0 0 Updated Aug 21, 2023
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