:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-generegionscan' .. highlight: bash bioconductor-generegionscan =========================== .. conda:recipe:: bioconductor-generegionscan :replaces_section_title: :noindex: GeneRegionScan :homepage: https://bioconductor.org/packages/3.18/bioc/html/GeneRegionScan.html :license: GPL (>= 2) :recipe: /`bioconductor-generegionscan `_/`meta.yaml `_ :links: biotools: :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. .. conda:package:: bioconductor-generegionscan |downloads_bioconductor-generegionscan| |docker_bioconductor-generegionscan| :versions: .. raw:: html
1.58.0-01.56.0-01.54.0-01.50.0-01.48.0-01.46.0-11.46.0-01.44.0-01.42.0-0 ``1.58.0-0``,  ``1.56.0-0``,  ``1.54.0-0``,  ``1.50.0-0``,  ``1.48.0-0``,  ``1.46.0-1``,  ``1.46.0-0``,  ``1.44.0-0``,  ``1.42.0-0``,  ``1.40.0-1``,  ``1.38.0-0``,  ``1.36.0-0``,  ``1.34.0-0`` .. raw:: html
:depends bioconductor-affxparser: ``>=1.74.0,<1.75.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-rcolorbrewer: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/bioconductor-generegionscan: (see `bioconductor-generegionscan/tags`_ for valid values for ````) .. |downloads_bioconductor-generegionscan| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-generegionscan.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-generegionscan :alt: (downloads) .. |docker_bioconductor-generegionscan| image:: https://quay.io/repository/biocontainers/bioconductor-generegionscan/status :target: https://quay.io/repository/biocontainers/bioconductor-generegionscan .. _`bioconductor-generegionscan/tags`: https://quay.io/repository/biocontainers/bioconductor-generegionscan?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html 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-generegionscan/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-generegionscan/README.html