This repository contains code used for the p50 infertility project. There are two separate tasks:
- Running CELLECT on ovary datasets with infertility and hormone GWAS sumstats to prioritise etiologic cell types.
- Finding marker genes for clusters from the ovary datasets.
- See datasets for more information on the datasets used for this part of the p50 project.
- The preprocessing directory contains code for
- filtering datasets to only include relevant samples
- creating h5seurat files (R Seurat object) from the scRNA-seq data required for finding cluster gene markers
- converting the h5seurat files to h5ad files (python Anndata object) to prepare for CELLEX. Where cell-type annotations are not availible online, the code includes clustering and annotating cell types using Seurat.