Multi-region exome sequencing analysis tool Kit

Intra-tumor heterogeneity (ITH) is now thought to be a key factor contributing to the therapeutic failures and drug resistance, which have attracted increasing attention in the cancer research field. Here, we present an R package, MesKit, for characterizing cancer genomic ITH and inferring the history of tumor evolution via implementation of well-established computational and statistical methods. The source code and documents are freely available through Github (https://github.com/Niinleslie/MesKit). A shiny application was developed to provide easier analysis and visualization.

Installation

# install via Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MesKit")

#  install the latest version from GitHub
if(!require(devtools)) install.packages("devtools")
devtools::install_github("Niinleslie/MesKit")

Usage

The structured documentation of MesKit can be found at http://meskit.renlab.org/.

Shiny APP

For GUI-based analysis, users can use the following code to launch Shiny app build with the package.

pkg.suggested <- c('shiny','shinyBS','shinydashboard', 'shinyWidgets', 'shinycssloaders', 'DT',
    'BSgenome.Hsapiens.UCSC.hg19')
## if genomic reference version is hg18/hg38, change 'BSgenome.Hsapiens.UCSC.hg19' to 'BSgenome.Hsapiens.UCSC.hg18' or 'BSgenome.Hsapiens.UCSC.hg38'

# Install the required packages
checkPackages <- function(pkg){
  if (!requireNamespace(pkg, quietly = TRUE)) {
    stop(paste0("Package ", pkg, " needed for shiny app. Please install it."), call. = FALSE)
  }
}
lapply(pkg.suggested, checkPackages)
# run shiny app from shiny package
shiny::runApp(system.file("shiny", package = "MesKit"))

Also, you can run the shiny interface by:

runMesKit()

The guidance video for MesKit Shiny APP can be found at http://meskit.renlab.org/video.html.

Configure Shiny APP with Docker

We provided a docker image for a quick configuration of shiny app bundle with shiny-server, please see the simple commands here.

Authors

This software was mainly developed by:

Mengni Liu, liumn5@mail2.sysu.edu.cn, Sun Yat-sen university
Jianyu Chen, chenjy327@mail2.sysu.edu.cn, Sun Yat-sen university
Xin Wang, wangx555@mail2.sysu.edu.cn, Sun Yat-sen university

Supervised by

Jian Ren and Qi Zhao from Bioinformatic Center of Sun Yat-sen University Cancer Center

Maintainer

Mengni Liu, Sun Yat-sen university

Copyright

Citation

Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Jian Ren, Qi Zhao, MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations, GigaScience, Volume 10, Issue 5, May 2021, giab036, https://doi.org/10.1093/gigascience/giab036