MesKit

DOI: 10.18129/B9.bioc.MesKit    

This is the development version of MesKit; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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 0.99.16
In Bioconductor since BioC 3.12 (R-4.0)
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_0.99.16.tar.gz
Windows Binary MesKit_0.99.16.zip
macOS 10.13 (High Sierra) MesKit_0.99.16.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

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