recipe bioconductor-scan.upc

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

Homepage:

https://bioconductor.org/packages/3.18/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:

2.44.0-0,  2.42.0-0,  2.40.0-0,  2.36.0-0,  2.34.0-0,  2.32.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-0, 

2.44.0-0,  2.42.0-0,  2.40.0-0,  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:

>=1.80.0,<1.81.0

depends bioconductor-affyio:

>=1.72.0,<1.73.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-geoquery:

>=2.70.0,<2.71.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-oligo:

>=1.66.0,<1.67.0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends r-base:

>=4.3,<4.4.0a0

depends r-foreach:

depends r-mass:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-scan.upc

and update with::

   mamba update bioconductor-scan.upc

To create a new environment, run:

mamba create --name myenvname bioconductor-scan.upc

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-scan.upc:<tag>

(see `bioconductor-scan.upc/tags`_ for valid values for ``<tag>``)

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