bioconductor-scan.upc

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SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.

Home http://bioconductor.org/packages/3.6/bioc/html/SCAN.UPC.html
Versions 2.18.0, 2.20.0
License MIT
Recipe https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-scan.upc

Installation

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

conda install bioconductor-scan.upc

and update with:

conda update bioconductor-scan.upc

docker

A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-scan.upc.