This repository contains the code used to analyse the data for the paper "Unified single-cell analysis of testis gene regulation and pathology in 5 mouse strains" doi:10.7554/eLife.43966.

For a quick start guide on using this package to explore the data check out the >>> vignette <<< (with pictures!).

To install this package, run:

remotes::install_github("myersgroup/testisAtlas")

The repository is structured as an R package. Generic functions that are used multiple times are in the R/ directory, other analysis scripts are in the analysis/ directory. Data used in the study is kept in the data/ directory but is not uploaded to github due to the large size. However R objects required to run the functions (e.g. "cell_data" a data.table containing cellwise metadata, and "SDAresults" a list object containing the results of the SDA composition) can be downloaded from: 10.5281/zenodo.3233870. The raw data is avaliable at GEO: GSE113293.

The shinyApp folder contains code for the web application for interactively exploring gene expression and components: http://www.stats.ox.ac.uk/~wells/testisAtlas.html