<img src="https://github.com/Niinleslie/MesKit/blob/mnliu/vignettes/logo.png" height="80" width="240" alt = "Github logo" /> # [M]()ulti-region [e]()xome [s]()equencing 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 ```R # 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/](http://meskit.renlab.org/). <div align="left"> <img src="https://github.com/Niinleslie/MesKit/blob/mnliu/vignettes/MesKit_workflow.png" height="500" width="600" alt = "MesKit Workflow"/> </div> ## Shiny APP For GUI-based analysis, users can use the following code to launch Shiny app build with the package. ```R 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: ```R 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](https://github.com/Niinleslie/MesKit/blob/master/MesKit.docker.md). ## 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](renjian@sysucc.org.cn) and [Qi Zhao](zhaoqi@sysucc.org.cn) from Bioinformatic Center of Sun Yat-sen University Cancer Center ## Maintainer [Mengni Liu](liumn5@mail2.sysu.edu.cn), Sun Yat-sen university <br/> ## Copyright Copyright © 2014-2021. RenLab from SYSUCC. All Rights Reserved<br/> For more useful tools/applications, please go to [renlab.org](http://www.renlab.org) ## Citation _MesKit: A Tool Kit for Dissecting Cancer Evolution of Multi-region Tumor Biopsies through Somatic Alterations (In production)_