Pathway Based Tumor Mutational Burden
draw an GenePathwayOncoplots
Filter cancer-specific dysfunction pathways.
Converts MAF into mutation matrix.
Calculate the Pathway-based Tumor Mutational Burden.
Drawing Kaplan Meier Survival Curves Using the final survival-related ...
Exact tests to detect mutually exclusive, co-occuring and altered gene...
plot the ROC curve
A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.