altcdfenvs
This is the released version of altcdfenvs; for the devel version, see altcdfenvs.
alternative CDF environments (aka probeset mappings)
Bioconductor version: Release (3.23)
Convenience data structures and functions to handle cdfenvs
Author: Laurent Gautier <lgautier at gmail.com>
Maintainer: Laurent Gautier <lgautier at gmail.com>
citation("altcdfenvs")):
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("altcdfenvs")
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("altcdfenvs")| altcdfenvs | R Script | |
| Alternative CDF environments for 2(or more)-genomes chips | R Script | |
| Modifying existing CDF environments to make alternative CDF environments | R Script | |
| Reference Manual |
Details
| biocViews | Annotation, Microarray, OneChannel, Preprocessing, ProprietaryPlatforms, QualityControl, Software, Transcription |
| Version | 2.74.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.7), methods, BiocGenerics(>= 0.1.0), S4Vectors(>= 0.9.25), Biobase(>= 2.15.1), affy, makecdfenv, Biostrings, hypergraph |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer |
| 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 | altcdfenvs_2.74.0.tar.gz |
| Windows Binary (x86_64) | altcdfenvs_2.74.0.zip |
| macOS Binary (big-sur-x86_64) | altcdfenvs_2.74.0.tgz |
| macOS Binary (sonoma-arm64) | altcdfenvs_2.74.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/altcdfenvs |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/altcdfenvs |
| Bioc Package Browser | https://code.bioconductor.org/browse/altcdfenvs/ |
| Package Short Url | https://bioconductor.org/packages/altcdfenvs/ |
| Package Downloads Report | Download Stats |