pathwayTMB: 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.

Version: 0.1.3
Depends: R (≥ 4.1.0)
Imports: BiocGenerics, 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
Published: 2022-08-09
DOI: 10.32614/CRAN.package.pathwayTMB
Author: Junwei Han [aut, cre, cph], Xiangmei Li [aut]
Maintainer: Junwei Han <hanjunwei1981 at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Language: en-US
In views: Omics
CRAN checks: pathwayTMB results


Reference manual: pathwayTMB.pdf
Vignettes: pathwayTMB


Package source: pathwayTMB_0.1.3.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): pathwayTMB_0.1.3.tgz, r-oldrel (arm64): pathwayTMB_0.1.3.tgz, r-release (x86_64): pathwayTMB_0.1.3.tgz, r-oldrel (x86_64): pathwayTMB_0.1.3.tgz
Old sources: pathwayTMB archive

Reverse dependencies:

Reverse imports: ProgModule


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