Package: SCAN.UPC
Type: Package
Title: Single-channel array normalization (SCAN) and Universal
        exPression Codes (UPC)
Version: 2.55.0
Author: Stephen R. Piccolo and Andrea H. Bild and W. Evan Johnson
Maintainer: Stephen R. Piccolo <stephen_piccolo@byu.edu>
Description: 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.
License: MIT
Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
        GEOquery, affy, affyio, foreach, sva
Suggests: pd.hg.u95a
Imports: utils, methods, MASS, tools, IRanges
URL: http://bioconductor.org, http://jlab.bu.edu/software/scan-upc
biocViews: ImmunoOncology, Software, Microarray, Preprocessing, RNASeq,
        TwoChannel, OneChannel
Config/pak/sysreqs: libicu-dev libpng-dev libxml2-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:36:55 UTC
RemoteUrl: https://github.com/bioc/SCAN.UPC
RemoteRef: HEAD
RemoteSha: 4626e5fe63209a324b3cdaef1b8bd7c74a41f1dc
NeedsCompilation: no
Packaged: 2026-05-30 09:53:37 UTC; root
Built: R 4.6.0; ; 2026-05-30 15:15:59 UTC; unix
