oligo
Preprocessing tools for oligonucleotide arrays
Bioconductor version: Release (3.17)
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Author: Benilton Carvalho and Rafael Irizarry
Maintainer: Benilton Carvalho <benilton at unicamp.br>
Citation (from within R, enter
citation("oligo")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("oligo")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("oligo")| oligo User's Guide | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, TwoChannel |
| Version | 1.64.1 |
| In Bioconductor since | BioC 2.0 (R-2.5) (16.5 years) |
| License | LGPL (>= 2) |
| Depends | R (>= 3.2.0), BiocGenerics(>= 0.13.11), oligoClasses(>= 1.29.6), Biobase(>= 2.27.3), Biostrings(>= 2.35.12) |
| Imports | affyio(>= 1.35.0), affxparser(>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore(>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc |
| Linking To | preprocessCore |
| Suggests | BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl |
| System Requirements | |
| Enhances | doMC, doMPI |
| URL |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | oligo_1.64.1.tar.gz |
| Windows Binary | oligo_1.64.1.zip |
| macOS Binary (x86_64) | oligo_1.64.1.tgz |
| macOS Binary (arm64) | oligo_1.64.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/oligo |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/oligo |
| Bioc Package Browser | https://code.bioconductor.org/browse/oligo/ |
| Package Short Url | https://bioconductor.org/packages/oligo/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |