Pathway Based Tumor Mutational Burden

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.


Reference manual

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0.1.1 by Junwei Han, 4 months ago

Browse source code at

Authors: Junwei Han [aut, cre, cph] , Xiangmei Li [aut]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports BiocGenerics, GenomicFeatures, purrr, utils, glmnet, randomForest, stats, survival, survminer, caret, data.table, RColorBrewer, grDevices, pROC, graphics, maftools, clusterProfiler

Suggests stringi, knitr, rmarkdown, testthat, BiocManager, xfun, e1071, qpdf, tinytex, spelling

See at CRAN