This repository contains code developed for the analysis presented in Shroff et al.
Scripts developed for the analysis of methylation data from mouse and in TCGA and Turkan et al.
Analysis of TF targets in differentially methylated regions (DMR).
Clustering of TCGA samples based on the murine gene expression signature.
Analysis of lineage signature enrichment in bulk RNA-seq data from the mouse model and human tumours from TCGA.
Deconvolution of the tumour microenvironment cell populations in bulk murine and TCGA data.
Analysis of T cell exclusion in bulk sequenced TCGA subgroups.
This code is free and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. See the GNU General Public License for more details.