This repository contains scripts used for the deconvolution analysis in Lazar-Contes et al., eLife 2024, Dynamics of transcriptional programs and chromatin accessibility in mouse spermatogonial cells from early postnatal to adult life (https://doi.org/10.7554/eLife.91528.3).
Prep_.R scripts
These scripts prepare the reference datasets, by processing single-cell RNA-seq data, performing clustering (if cluster IDs are not provided by the original publication), and generating reference files for CIBERSORTx.
Deconvolution.R
This script runs the deconvolution analysis (CIBERSORTx) using the bulk RNA-seq dataset in Lazar-Contes et al., 2024 and all of the prepared reference datasets.