tidyselect (>= 1.1.0), cowplot, anomalize, lubridate

Title: Pathway Based Tumor Mutational Burden
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.
Imports: maftools, clusterProfiler, BiocGenerics, GenomicFeatures,
purrr, utils, glmnet, randomForest, stats, survival, survminer,
caret, data.table, RColorBrewer, grDevices, pROC, graphics
Suggests: stringi, knitr, rmarkdown, testthat, BiocManager, xfun,

Imports: BiocGenerics, GenomicFeatures, purrr, utils, glmnet,
randomForest, stats, survival, survminer, caret, data.table,
RColorBrewer, grDevices, pROC, graphics, maftools,

Imports: BiocGenerics, purrr, utils, glmnet, randomForest, stats,
survival, survminer, caret, data.table, RColorBrewer,
grDevices, pROC, graphics, maftools, clusterProfiler

Title: Visualization of Patient Profiles
Authors@R: c(person(given = "Laure", family = "Cougnaud", role = c("aut", "cre"), email = "laure.cougnaud@openanalytics.eu"), person(given = "Open Analytics", role = "cph"))
Description: Creation of patient profile visualizations for
exploration, diagnostic or monitoring purposes during a clinical trial.
These static visualizations display a patient-specific overview
of the evolution during the trial time frame of
parameters of interest (as laboratory, ECG, vital signs),
presence of adverse events, exposure to a treatment;
associated with metadata patient information,
The visualizations can be tailored for specific domain(s) or endpoint(s) of interest.
Visualizations are exported into patient profile report(s)
Imports: clinUtils, ggplot2 (>= 3.0.0), plyr, cowplot, tools, reshape2,
knitr, grid, dplyr, stringr, parallel, gridExtra, scales
Suggests: pander, shiny, testthat, grDevices, rmarkdown, gtable,
Packaged: 2021-06-11 11:26:24 UTC; lcougnaud