MSTree
This is the development version of MSTree; to use it, please install the devel version of Bioconductor.
MSTree plotting minimum spanning tree directly from the output of ChewBBACA pipeline
Bioconductor version: Development (3.24)
This package is used to generate a graph object from the output of chewBBACA pipeline (https://chewbbaca.readthedocs.io/en/latest/). Then, the generated graph object can be used to make a minimum spanning tree (MST). The minimum spanning tree can be customized using all the available arguments. This package consists of two functions: one to build the graph and another one for plotting.
Author: Abdullah El-Kurdi [aut, cre]
Maintainer: Abdullah El-Kurdi <ak161 at aub.edu.lb>
citation("MSTree")):
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("MSTree")
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("MSTree")| MSTree | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, ComparativeGenomics, GenomicVariation, Software |
| Version | 0.99.6 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | |
| Imports | igraph, ggraph, ggplot2, utils, methods, NetPathMiner |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, testthat, BiocGenerics, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MSTree_0.99.6.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | MSTree_0.99.6.tgz |
| macOS Binary (sonoma-arm64) | MSTree_0.99.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSTree |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSTree |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSTree/ |
| Package Short Url | https://bioconductor.org/packages/MSTree/ |
| Package Downloads Report | Download Stats |