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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>
Citation (from within R,
enter citation("MesKit")
):
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.
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 |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
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 |
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 |
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