MesKit

This is the development version of MesKit; for the stable release version, see MesKit.

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

Bioconductor version: Development (3.21)

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] (ORCID: ), Jianyu Chen [aut, ctb] (ORCID: ), Xin Wang [aut, ctb] (ORCID: )

Maintainer: Mengni Liu <niinleslie at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Software
Version	1.17.0
In Bioconductor since	BioC 3.12 (R-4.0) (4 years)
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
System Requirements
URL

Suggests	shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), org.Hs.eg.db, clusterProfiler, TxDb.Hsapiens.UCSC.hg19.knownGene
Linking To
Enhances
Depends On Me
Imports Me	CaMutQC
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MesKit_1.17.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MesKit
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MesKit
Bioc Package Browser	https://code.bioconductor.org/browse/MesKit/
Package Short Url	https://bioconductor.org/packages/MesKit/
Package Downloads Report	Download Stats