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: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=pathwayTMB to link to this page.
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