affycoretools
This is the development version of affycoretools; for the stable release version, see affycoretools.
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Bioconductor version: Development (3.21)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | GeneExpression, Microarray, OneChannel, ReportWriting, Software |
| Version | 1.79.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (18.5 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, Glimma |
| System Requirements | |
| URL |
See More
| Suggests | affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown |
| 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 | affycoretools_1.79.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |