DeSousa2013
This is the released version of DeSousa2013; for the devel version, see DeSousa2013.
Poor prognosis colon cancer is defined by a molecularly distinct subtype and precursor lesion
Bioconductor version: Release (3.23)
This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013.
Author: Xin Wang <Xin.Wang at cruk.cam.ac.uk>
Maintainer: Xin Wang <Xin.Wang at cruk.cam.ac.uk>
citation("DeSousa2013")):
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("DeSousa2013")
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("DeSousa2013")| Main vignette:Poor prognosis colon cancer is defined by a molecular distinct subtype and develops from serrated precursor lesions | R Script | |
| Reference Manual |
Details
| biocViews | CancerData, ColonCancerData, ExperimentData, MicroarrayData |
| Version | 1.48.0 |
| License | Artistic-2.0 |
| Depends | R (>= 2.15) |
| Imports | affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs, sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr, survival, gplots, AnnotationDbi, Biobase |
| System Requirements | |
| URL |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DeSousa2013_1.48.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/DeSousa2013 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DeSousa2013 |
| Package Short Url | https://bioconductor.org/packages/DeSousa2013/ |
| Package Downloads Report | Download Stats |