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 (3.24)
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>
citation("MesKit")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 |
See More
| 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | MesKit_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | MesKit_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | MesKit_1.23.0.tgz |
| 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 |