Package: pathwayTMB
Type: Package
Title: Pathway Based Tumor Mutational Burden
Version: 0.1.3
Maintainer: Junwei Han <hanjunwei1981@163.com>
Authors@R: c(person(given = "Junwei", family = "Han", email = "hanjunwei1981@163.com", role  = c("aut", "cre", "cph")),
             person(given = "Xiangmei", family = "Li", role  = "aut"))
Description: 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.
License: GPL (>= 2)
Depends: R (>= 4.1.0)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
biocViews:
Imports: BiocGenerics, purrr, utils, glmnet, randomForest, stats,
        survival, survminer, caret, data.table, RColorBrewer,
        grDevices, pROC, graphics, maftools, clusterProfiler
VignetteBuilder: knitr,rmarkdown,qpdf
Suggests: stringi, knitr, rmarkdown, testthat, BiocManager, xfun,
        e1071, qpdf, tinytex, spelling
Language: en-US
NeedsCompilation: no
Packaged: 2022-08-01 13:54:24 UTC; DELL
Author: Junwei Han [aut, cre, cph],
  Xiangmei Li [aut]
Repository: CRAN
Date/Publication: 2022-08-09 13:50:02 UTC
