recipe bioconductor-panp

Presence-Absence Calls from Negative Strand Matching Probesets

Homepage

https://bioconductor.org/packages/3.14/bioc/html/panp.html

License

GPL (>= 2)

Recipe

/bioconductor-panp/meta.yaml

Links

biotools: panp, doi: 10.1109/BIBE.2007.4375552

A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

package bioconductor-panp

Versions

1.64.0-0,  1.62.0-0,  1.60.0-1,  1.60.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-1,  1.52.0-0,  1.50.0-0, 

1.64.0-0,  1.62.0-0,  1.60.0-1,  1.60.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-0

Depends

• bioconductor-affy >=1.72.0,<1.73.0

• bioconductor-biobase >=2.54.0,<2.55.0

• 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-panp

and update with:

conda update bioconductor-panp

or use the docker container:

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

(see bioconductor-panp/tags for valid values for <tag>)

Download stats

Link to this page

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