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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 ( A shiny application was developed to provide easier analysis and visualization.


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


#  install the latest version from GitHub
if(!require(devtools)) install.packages("devtools")


The structured documentation of MesKit can be found at

MesKit Workflow

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',
## 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:


The guidance video for MesKit Shiny APP can be found at

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.


This software was mainly developed by:

Supervised by


Mengni Liu, Sun Yat-sen university


Copyright © 2014-2021. RenLab from SYSUCC. All Rights Reserved For more useful tools/applications, please go to


MesKit: A Tool Kit for Dissecting Cancer Evolution of Multi-region Tumor Biopsies through Somatic Alterations (Under revision)

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MesKit documentation built on March 28, 2021, 6 p.m.