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.


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install.packages("pathwayTMB")

0.1.0 by Junwei Han, 2 months ago


Browse source code at https://github.com/cran/pathwayTMB


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


Documentation:   PDF Manual  


GPL (>= 2) license


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

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


See at CRAN