recipe bioconductor-scan.upc

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Homepage

https://bioconductor.org/packages/3.13/bioc/html/SCAN.UPC.html

License

MIT

Recipe

/bioconductor-scan.upc/meta.yaml

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

2.34.0-0,  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, 

2.34.0-0,  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 >=1.70.0,<1.71.0

• bioconductor-affyio >=1.62.0,<1.63.0

• bioconductor-biobase >=2.52.0,<2.53.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-geoquery >=2.60.0,<2.61.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-oligo >=1.56.0,<1.57.0

• bioconductor-sva >=3.40.0,<3.41.0

• r-base >=4.1,<4.2.0a0

• r-foreach

• r-mass

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

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