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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "SCAN.UPC" in publications use:'
type: software
license: MIT
title: 'SCAN.UPC: Single-channel array normalization (SCAN) and Universal exPression
  Codes (UPC)'
version: 2.47.0
doi: 10.1016/j.ygeno.2012.08.003
abstract: 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.
authors:
- family-names: Piccolo
  given-names: Stephen R.
  email: stephen_piccolo@byu.edu
- family-names: Piccolo
  given-names: Stephen R.
- family-names: Bild
  given-names: Andrea H.
- family-names: Johnson
  given-names: W. Evan
preferred-citation:
  type: article
  title: A single-sample microarray normalization method to facilitate personalized-medicine
    workflows
  authors:
  - family-names: Piccolo
    given-names: Stephen R.
    email: stephen_piccolo@byu.edu
  - family-names: Sun
    given-names: Ying
  - family-names: Campbell
    given-names: Joshua D.
  - family-names: Lenburg
    given-names: Marc E.
  - family-names: Bild
    given-names: Andrea H.
  - family-names: Johnson
    given-names: W. Evan
  journal: Genomics
  volume: '100'
  issue: '6'
  year: '2012'
  doi: 10.1016/j.ygeno.2012.08.003
  publisher:
    name: Elsevier
    address: Oxford, UK
  start: 337-344
repository: https://bioc.r-universe.dev
url: http://bioconductor.org
contact:
- family-names: Piccolo
  given-names: Stephen R.
  email: stephen_piccolo@byu.edu
references:
- type: article
  title: Multi-platform single-sample estimates of transcriptional activation
  authors:
  - family-names: Piccolo
    given-names: Stephen R.
  - family-names: Withers
    given-names: Michelle R.
  - family-names: Francis
    given-names: Owen E.
  - family-names: Bild
    given-names: Andrea H.
  - family-names: Johnson
    given-names: W. Evan
  journal: Proceedings of the National Academy of Sciences of the United States of
    America
  volume: '110'
  issue: '44'
  year: '2013'
  doi: 10.1016/j.ygeno.2012.08.003
  start: 17778-17783
identifiers:
- type: url
  value: http://jlab.bu.edu/software/scan-upc