affxparser

Affymetrix File Parsing SDK

Bioconductor version: Release (3.20)

Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.

Author: Henrik Bengtsson [aut], James Bullard [aut], Robert Gentleman [ctb], Kasper Daniel Hansen [aut, cre], Jim Hester [ctb], Martin Morgan [ctb]

Maintainer: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>

Citation (from within R, enter citation("affxparser")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("affxparser")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Infrastructure, Microarray, OneChannel, ProprietaryPlatforms, Software
Version	1.78.0
In Bioconductor since	BioC 1.7 (R-2.2) (19 years)
License	LGPL (>= 2)
Depends	R (>= 2.14.0)
Imports
System Requirements
URL	https://github.com/HenrikBengtsson/affxparser
Bug Reports	https://github.com/HenrikBengtsson/affxparser/issues

Suggests	R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
Linking To
Enhances
Depends On Me	ITALICS, pdInfoBuilder
Imports Me	affyILM, cn.farms, EventPointer, GeneRegionScan, ITALICS, oligo
Suggests Me	TIN, aroma.affymetrix, aroma.apd
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	affxparser_1.78.0.tar.gz
Windows Binary (x86_64)	affxparser_1.78.0.zip (64-bit only)
macOS Binary (x86_64)	affxparser_1.78.0.tgz
macOS Binary (arm64)	affxparser_1.78.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/affxparser
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/affxparser
Bioc Package Browser	https://code.bioconductor.org/browse/affxparser/
Package Short Url	https://bioconductor.org/packages/affxparser/
Package Downloads Report	Download Stats