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 (3.12)

MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to decipher ITH, infer metastatic routes as well as uncover the underlying process of mutagenesis. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the understanding of cancer cell evolution and its relevance to cancer therapeutics.

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 "4.0") 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	Classification, DataRepresentation, GUI, GeneticVariability, Genetics, Sequencing, Software, SomaticMutation, VariantAnnotation, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.0.0)
Imports	methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape, ggrepel, pracma, ggridges, 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
SystemRequirements
Enhances
URL
BugReports	https://github.com/Niinleslie/MesKit/issues
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_1.0.0.tar.gz
Windows Binary	MesKit_1.0.0.zip
macOS 10.13 (High Sierra)	MesKit_1.0.0.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