MesKit

DOI: 10.18129/B9.bioc.MesKit    

A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Bioconductor version: Release (3.13)

MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to depict mutational profiles, measure heterogeneity within or between tumors from the same patient, track evolutionary dynamics, as well as characterize mutational patterns on different levels. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the interpretation of tumor heterogeneity and the understanding of evolutionary relationship between regions in MRS study.

Author: Mengni Liu [aut, cre] , Jianyu Chen [aut, ctb] , Xin Wang [aut, ctb]

Maintainer: Mengni Liu <niinleslie at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("MesKit")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MesKit")

 

HTML	R Script	Analyze and Visualize Multi-region Whole-exome Sequencing Data
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Software
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape (>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges, circlize, cowplot, mclust, phangorn, ComplexHeatmap(>= 1.9.3), ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors
LinkingTo
Suggests	shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19(>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MesKit_1.2.0.tar.gz
Windows Binary	MesKit_1.2.0.zip
macOS 10.13 (High Sierra)	MesKit_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MesKit
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MesKit
Package Short Url	https://bioconductor.org/packages/MesKit/
Package Downloads Report	Download Stats