messina
This is the released version of messina; for the devel version, see messina.
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems
Bioconductor version: Release (3.23)
Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.
Author: Mark Pinese [aut], Mark Pinese [cre], Mark Pinese [cph]
Maintainer: Mark Pinese <mpinese at ccia.org.au>
citation("messina")):
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("messina")
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("messina")| Using Messina | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, Classification, DifferentialExpression, GeneExpression, Software, Survival |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | EPL (>= 1.0) |
| Depends | R (>= 3.1.0), survival (>= 2.37-4), methods |
| Imports | Rcpp (>= 0.11.1), plyr (>= 1.8), ggplot2 (>= 0.9.3.1), grid (>= 3.1.0), foreach (>= 1.4.1), graphics |
| System Requirements | |
| URL |
See More
| Suggests | knitr (>= 1.5), antiProfilesData(>= 0.99.2), Biobase(>= 2.22.0), BiocStyle |
| Linking To | Rcpp |
| Enhances | doMC (>= 1.3.3) |
| 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 | messina_1.48.0.tar.gz |
| Windows Binary (x86_64) | messina_1.48.0.zip |
| macOS Binary (big-sur-x86_64) | messina_1.48.0.tgz |
| macOS Binary (sonoma-arm64) | messina_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/messina |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/messina |
| Bioc Package Browser | https://code.bioconductor.org/browse/messina/ |
| Package Short Url | https://bioconductor.org/packages/messina/ |
| Package Downloads Report | Download Stats |