affxparser

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see affxparser.

Affymetrix File Parsing SDK

Bioconductor version: 3.8

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 "3.5") 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 1.54.0

In Bioconductor since BioC 1.7 (R-2.2) (18.5 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, rMAT, Starr

Imports Me affyILM, cn.farms, crossmeta, EventPointer, GeneRegionScan, ITALICS, oligo, rMAT

Suggests Me TIN

Links To Me

Build Report Build Report

Package Archives

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

Source Package affxparser_1.54.0.tar.gz

Windows Binary affxparser_1.54.0.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) affxparser_1.54.0.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

Old Source Packages for BioC 3.8 Source Archive