recipe bioconductor-xps

Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Homepage

https://bioconductor.org/packages/3.10/bioc/html/xps.html

License

GPL (>= 2.0)

Recipe

/bioconductor-xps/meta.yaml

The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.

package bioconductor-xps

(downloads) docker_bioconductor-xps

Versions

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-xps

and update with:

conda update bioconductor-xps

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-xps:<tag>

(see bioconductor-xps/tags for valid values for <tag>)