This code has been developed to investigate the immunity lanscape of primary head & neck squamous cell carcinomas, as presented in the manuscript "Immune cell abundance and T cell receptor landscapes suggest new patient stratification strategies in head and neck squamous cell carcinoma" (Secrier et al).
The scripts employed in this analysis are as follows:
immuneDeconvolution.R - performs immune deconvolution in the cohort from expression data and defines the immunity groups
immuneValidationInTCGA.R - validates the uncovered immune groups in TCGA
immunityAnalysisByGroup.R - further analysis of the immunity groups in relation to clinical and genomic parameters
generalImmunityAnalysis.R - analysis of TLS enrichment in the immune groups, and links to molecular measurements via IHC
snvs_oncoprint.Rmd - generates an oncoprint of genomic changes in the overall cohort
mutSignatures_analysis.Rmd - infers mutational signatures acting in the tumours analysed in this study
snvs_oncoprint_RTK.Rmd - generates an oncoprint of genomic changes across genes in the Ras/ERK and PI3K/AKT pathways
expressionAnalysis_CTME_highVSlow.Rmd - modelling of immunity based on expression changes in genes across the Ras/ERK and PI3K/AKT pathways
coxPH_analysis_CTME.Rmd - Cox Proportional Hazards modelling of patient outcomes taking into account immunity
Operating system(s): Unix (linux, mac) Programming Language: R
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.