ninomoriaty/meskit repository overview

⁠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. MesKit provides a wide range of analysis including ITH evaluation, enrichment, signature, clone evolution analysis via implementation of well-established computational and statistical methods. The source code and documents are freely available through Github (https://github.com/Niinleslie/MesKit⁠). We also developed a shiny application to provide easier analysis and visualization.

⁠Installation

install.packages("remotes")
remotes::install_github("Niinleslie/MesKit")

⁠Usage

A complete documentation of MesKit can be found here.⁠

⁠Shiny APP

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

pkg.suggested <- c('shiny', 'shinyjs','shinyBS','shinydashboard', 'shinyWidgets', 'shinycssloaders', 'DT','org.Hs.eg.db','BSgenome.Hsapiens.UCSC.hg19')
## if genomic reference version is hg38, change 'BSgenome.Hsapiens.UCSC.hg19' to 'BSgenome.Hsapiens.UCSC.hg38'

# Install the required packages
checkPackages <- function(pkg){
  if (!requireNamespace(pkg, quietly = TRUE)) {
    stop("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 shiny with:

runMesKit()

⁠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, [email protected]⁠, Sun Yat-sen university
• Chengwei Wang, [email protected]⁠, Sun Yat-sen university
• Jianyu Chen, [email protected]⁠, Sun Yat-sen university
• Xin Wang, [email protected]⁠, 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

Copyright © 2014-2019. RenLab from SYSUCC. All Rights Reserved
For more useful tools/applications, please go to renlab.org⁠

⁠Citation

Citation (from within R, enter citation("MesKit")):

MesKit: a tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations