- recipe bioconductor-scan.upc
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
- Homepage
https://bioconductor.org/packages/3.14/bioc/html/SCAN.UPC.html
- License
MIT
- Recipe
- Links
biotools: 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.
- package bioconductor-scan.upc¶
-
- Versions
2.36.0-0
,2.34.0-0
,2.32.0-1
,2.32.0-0
,2.30.0-0
,2.28.0-0
,2.26.0-1
,2.24.1-0
,2.22.0-0
,2.36.0-0
,2.34.0-0
,2.32.0-1
,2.32.0-0
,2.30.0-0
,2.28.0-0
,2.26.0-1
,2.24.1-0
,2.22.0-0
,2.20.0-0
,2.18.0-0
- Depends
bioconductor-affy
>=1.72.0,<1.73.0
bioconductor-affyio
>=1.64.0,<1.65.0
bioconductor-biobase
>=2.54.0,<2.55.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-geoquery
>=2.62.0,<2.63.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-oligo
>=1.58.0,<1.59.0
bioconductor-sva
>=3.42.0,<3.43.0
r-base
>=4.1,<4.2.0a0
- 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-scan.upc/README.html)