-
recipe
bioconductor-scan.upc¶ 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.
- Homepage
https://bioconductor.org/packages/3.9/bioc/html/SCAN.UPC.html
- License
MIT
- Recipe
- Links
biotools: scan.upc
-
package
bioconductor-scan.upc¶ 
- Versions
2.24.1-0, 2.22.0-0, 2.20.0-0, 2.18.0-0
- Depends
bioconductor-affy >=1.60.0,<1.61.0
bioconductor-affyio >=1.52.0,<1.53.0
bioconductor-biobase >=2.42.0,<2.43.0
bioconductor-biostrings >=2.50.0,<2.51.0
bioconductor-geoquery >=2.50.0,<2.51.0
bioconductor-iranges >=2.16.0,<2.17.0
bioconductor-oligo >=1.46.0,<1.47.0
bioconductor-sva >=3.30.0,<3.31.0
r-base >=3.5.1,<3.5.2.0a0
- Required By
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
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-scan.upc:<tag>
(see bioconductor-scan.upc/tags for valid values for
<tag>)
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-scan.upc/README.html)