recipe bioconductor-paa

PAA (Protein Array Analyzer)

Homepage

https://bioconductor.org/packages/3.10/bioc/html/PAA.html

License

BSD_3_clause + file LICENSE

Recipe

/bioconductor-paa/meta.yaml

PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the “minimum M statistic” approach - hereinafter referred to as “mMs”). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.

package bioconductor-paa

Versions

1.20.0-0, 1.18.0-1, 1.16.0-0

Depends

• bioconductor-limma >=3.42.0,<3.43.0

• bioconductor-sva >=3.34.0,<3.35.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• r-e1071

• r-gplots

• r-gtools

• r-mass

• r-mrmre

• r-randomforest

• r-rcpp >=0.11.6

• r-rocr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-paa

and update with:

conda update bioconductor-paa

or use the docker container:

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

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

Link to this page

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