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 163.com>
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	no
Language:	en-US
In views:	Omics
CRAN checks:	pathwayTMB results

Documentation:

Reference manual:	pathwayTMB.pdf
Vignettes:	pathwayTMB

Downloads:

Package source:	pathwayTMB_0.1.3.tar.gz
Windows binaries:	r-devel: pathwayTMB_0.1.3.zip, r-release: pathwayTMB_0.1.3.zip, r-oldrel: pathwayTMB_0.1.3.zip
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

Linking:

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