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 |
Reference manual: | pathwayTMB.pdf |
Vignettes: |
pathwayTMB |
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 imports: | ProgModule |
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