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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("makecdfenv")
In most cases, you don't need to download the package archive at all.
makecdfenv
CDF Environment Maker
Bioconductor version: 3.0
This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.
Author: Rafael A. Irizarry <rafa at jhu.edu>, Laurent Gautier <laurent at cbs.dtu.dk>, Wolfgang Huber <w.huber at dkfz-heidelberg.de>, Ben Bolstad <bmb at bmbolstad.com>
Maintainer: James W. MacDonald <jmacdon at u.washington.edu>
Citation (from within R,
enter citation("makecdfenv")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("makecdfenv")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("makecdfenv")
| R Script | makecdfenv primer | |
| Reference Manual |
Details
| biocViews | DataImport, OneChannel, Preprocessing, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier |
| License | GPL (>= 2) |
| Depends | R (>= 2.6.0), affyio |
| Imports | Biobase, affy, methods, stats, utils, zlibbioc |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | altcdfenvs |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | makecdfenv_1.42.0.tar.gz |
| Windows Binary | makecdfenv_1.42.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | makecdfenv_1.42.0.tgz |
| Mac OS X 10.9 (Mavericks) | makecdfenv_1.42.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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