recipe bioconductor-panp

Presence-Absence Calls from Negative Strand Matching Probesets

Homepage:

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

(downloads) docker_bioconductor-panp

versions:
1.72.0-0,  1.70.0-0,  1.68.0-0,  1.64.0-0,  1.62.0-0,  1.60.0-1,  1.60.0-0,  1.58.0-0,  1.56.0-0, 

1.72.0-0,  1.70.0-0,  1.68.0-0,  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:

>=1.80.0,<1.81.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends r-base:

>=4.3,<4.4.0a0

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-panp

and update with::

   mamba update bioconductor-panp

To create a new environment, run:

mamba create --name myenvname bioconductor-panp

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-panp:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-panp/README.html)