recipe bioconductor-generegionscan




GPL (>= 2)




biotools: generegionscan

A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

package bioconductor-generegionscan

(downloads) docker_bioconductor-generegionscan



depends bioconductor-affxparser:


depends bioconductor-biobase:


depends bioconductor-biostrings:


depends bioconductor-s4vectors:


depends r-base:


depends r-rcolorbrewer:



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-generegionscan

and update with::

   mamba update bioconductor-generegionscan

To create a new environment, run:

mamba create --name myenvname bioconductor-generegionscan

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<tag>

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

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