SUITOR
This is the released version of SUITOR; for the devel version, see SUITOR.
Selecting the number of mutational signatures through cross-validation
Bioconductor version: Release (3.23)
An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data.
Author: DongHyuk Lee [aut], Bin Zhu [aut], Bill Wheeler [cre]
Maintainer: Bill Wheeler <wheelerb at imsweb.com>
citation("SUITOR")):
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")
BiocManager::install("SUITOR")
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("SUITOR")| SUITOR: selecting the number of mutational signatures | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Genetics, Software, SomaticMutation |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-2 |
| Depends | R (>= 4.2.0) |
| Imports | stats, utils, graphics, ggplot2, BiocParallel |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/wheelerb/SUITOR/issues |
See More
| Suggests | devtools, MutationalPatterns, RUnit, BiocManager, 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 | SUITOR_1.14.0.tar.gz |
| Windows Binary (x86_64) | SUITOR_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | SUITOR_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | SUITOR_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SUITOR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SUITOR |
| Bioc Package Browser | https://code.bioconductor.org/browse/SUITOR/ |
| Package Short Url | https://bioconductor.org/packages/SUITOR/ |
| Package Downloads Report | Download Stats |