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@mccoy-lab

mccoy-lab

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  1. 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 36 3

  2. karyohmm Public

    Implementation of the karyoHMM model for assessing aneuploidy in PGT data

    Python

  3. 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 17

  4. t2t-variants Public

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

    R 17 3

  5. hgv_modules Public

    Teaching modules for Human Genome Variation Lab.

    R 20 3

  6. 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 18 repositories
  • aneuploidyRates Public

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

    R 1 1 0 1 Updated Apr 20, 2025
  • natera_recomb Public
    Jupyter Notebook 0 0 3 0 Updated Apr 9, 2025
  • natera_aneuploidy Public

    GWAS + QuantGen of Aneuploidy in Natera PGT Data

    Jupyter Notebook 0 0 0 0 Updated Apr 9, 2025
  • karyohmm Public

    Implementation of the karyoHMM model for assessing aneuploidy in PGT data

    Python 0 0 6 (2 issues need help) 1 Updated Apr 2, 2025
  • 1kgp_chm13_maps Public
    R 1 0 0 0 Updated Feb 19, 2025
  • hgv_modules Public

    Teaching modules for Human Genome Variation Lab.

    R 20 CC-BY-4.0 3 0 0 Updated Jul 31, 2024
  • 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 36 3 0 0 Updated Jul 19, 2024
  • LD-CHASE Public

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

    Python 4 0 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

    R 1 0 0 0 Updated Aug 21, 2023
  • t2t-variants Public

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

    R 17 3 1 0 Updated Jan 17, 2023
View all repositories