recipe bioconductor-paa

PAA (Protein Array Analyzer)

Homepage:

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

1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.28.0-2,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1, 

1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.28.0-2,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-limma:

>=3.58.1,<3.59.0a0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends bioconductor-sva:

>=3.50.0,<3.51.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-e1071:

depends r-gplots:

depends r-gtools:

depends r-mass:

depends r-mrmre:

depends r-randomforest:

depends r-rcpp:

>=0.11.6

depends r-rocr:

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-paa

and update with::

   mamba update bioconductor-paa

To create a new environment, run:

mamba create --name myenvname bioconductor-paa

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-paa:<tag>

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

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