README.md

In gmelloni/PrecisionTrialDesigner: A Tool to Analyze and Design NGS Based Custom Gene Panels

PrecisionTrialDrawer

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.

Install

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")

Info

For an explanation of the package functionalities, refer to the official website: https://gmelloni.github.io/ptd/

Web resource

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.

gmelloni/PrecisionTrialDesigner documentation built on March 3, 2023, 6:10 a.m.