affycoretools
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see affycoretools.
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Bioconductor version: 3.9
Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.
Author: James W. MacDonald
Maintainer: James W. MacDonald <jmacdon at u.washington.edu>
Citation (from within R, enter
citation("affycoretools")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("affycoretools")
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("affycoretools")| Creating annotated output with \Biocpkg{affycoretools} and ReportingTools | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Microarray, OneChannel, ReportWriting, Software |
| Version | 1.56.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (18 years) |
| License | Artistic-2.0 |
| Depends | Biobase, methods |
| Imports | affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi, ggplot2, gplots, oligoClasses, ReportingTools, hwriter, lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI |
| System Requirements | |
| URL |
See More
| Suggests | affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | AgiMicroRna |
| 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 | affycoretools_1.56.0.tar.gz |
| Windows Binary | affycoretools_1.56.0.zip |
| Mac OS X 10.11 (El Capitan) | affycoretools_1.56.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/affycoretools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/affycoretools |
| Bioc Package Browser | https://code.bioconductor.org/browse/affycoretools/ |
| Package Short Url | https://bioconductor.org/packages/affycoretools/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |