A set of tools to help bioinformaticians, clinicians and biostatisticians to design, analyze and finalize a custom gene panel for clinical trial in cancer genomics.
You can install PrecisionTrialDrawer using devtools
install.packages("devtools")
devtools::install_github("gmelloni/PrecisionTrialDrawer")
In case some of the dependencies are not automatically downloaded, you can install the dependencies first and then run install_github
source("https://bioconductor.org/biocLite.R")
biocLite(c('cBioPortalData','parallel','stringr',
'reshape2','data.table','RColorBrewer',
'BiocParallel','magrittr','biomaRt',
'XML','httr','jsonlite',
'ggplot2','ggrepel','grid',
'S4Vectors','IRanges','GenomicRanges',
'googleVis','shiny',
'shinyBS','DT','brglm','BiocStyle',
'knitr','rmarkdown','dplyr','testthat'))
biocLite('LowMACAAnnotation')
devtools::install_github("gmelloni/PrecisionTrialDrawer")
For an explanation of the package functionalities, refer to the official website: https://gmelloni.github.io/ptd/
A demo version of PTD is available as a web resource here. The web version is meant for demonstration purpose and only a limited group of functionalities are implemented.