mccoy-lab

MAGE

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

hgv_modules

Teaching modules for Human Genome Variation Lab.

t2t-variants

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

LD-PGTA

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

aneuploidy_scrnaseq

Detection of aneuploidy using scRNA-seq data from human embryos.

sv_selection

Code for Yan et al., "Local adaptation and archaic introgression shape global diversity at human structural variant loci."

rhapsodi

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

LD-CHASE

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

embryo_arrest

Meiotic and mitotic aneuploidies drive preimplantation mortality of in vitro fertilized human embryos

transmission-distortion

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

CSHL_seqtec_2022

pot1_ch_2022

Code for DeBoy & Tassia et al., Familial clonal hematopoiesis in a long telomere syndrome.

sQTLviz

visualising LeafCutter sQTLs by genotype

aneuploidyRates

A repository for an R package that estimates the meiotic and mitotic aneuploidy rates of an embryo