:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-ringo' .. highlight: bash bioconductor-ringo ================== .. conda:recipe:: bioconductor-ringo :replaces_section_title: :noindex: R Investigation of ChIP\-chip Oligoarrays :homepage: https://bioconductor.org/packages/3.18/bioc/html/Ringo.html :license: Artistic-2.0 :recipe: /`bioconductor-ringo `_/`meta.yaml `_ :links: biotools: :biotools:`ringo` The package Ringo facilitates the primary analysis of ChIP\-chip data. The main functionalities of the package are data read\-in\, quality assessment\, data visualisation and identification of genomic regions showing enrichment in ChIP\-chip. The package has functions to deal with two\-color oligonucleotide microarrays from NimbleGen used in ChIP\-chip projects\, but also contains more general functions for ChIP\-chip data analysis\, given that the data is supplied as RGList \(raw\) or ExpressionSet \(pre\- processed\). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP\-chip\-specific and NimbleGen\-specific functionalities. .. conda:package:: bioconductor-ringo |downloads_bioconductor-ringo| |docker_bioconductor-ringo| :versions: .. raw:: html
1.66.0-01.64.0-01.62.0-11.62.0-01.58.0-21.58.0-11.58.0-01.56.0-01.54.0-1 ``1.66.0-0``,  ``1.64.0-0``,  ``1.62.0-1``,  ``1.62.0-0``,  ``1.58.0-2``,  ``1.58.0-1``,  ``1.58.0-0``,  ``1.56.0-0``,  ``1.54.0-1``,  ``1.54.0-0``,  ``1.52.0-0``,  ``1.50.0-0``,  ``1.48.0-1``,  ``1.46.0-0``,  ``1.44.0-0``,  ``1.42.0-0``,  ``1.40.0-0``,  ``1.38.0-1``,  ``1.38.0-0`` .. raw:: html
:depends bioconductor-biobase: ``>=2.62.0,<2.63.0`` :depends bioconductor-biobase: ``>=2.62.0,<2.63.0a0`` :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0`` :depends bioconductor-biocgenerics: ``>=0.48.1,<0.49.0a0`` :depends bioconductor-genefilter: ``>=1.84.0,<1.85.0`` :depends bioconductor-genefilter: ``>=1.84.0,<1.85.0a0`` :depends bioconductor-limma: ``>=3.58.0,<3.59.0`` :depends bioconductor-limma: ``>=3.58.1,<3.59.0a0`` :depends bioconductor-vsn: ``>=3.70.0,<3.71.0`` :depends bioconductor-vsn: ``>=3.70.0,<3.71.0a0`` :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-lattice: :depends r-matrix: :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-ringo and update with:: mamba update bioconductor-ringo To create a new environment, run:: mamba create --name myenvname bioconductor-ringo 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-ringo: (see `bioconductor-ringo/tags`_ for valid values for ````) .. |downloads_bioconductor-ringo| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-ringo.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-ringo :alt: (downloads) .. |docker_bioconductor-ringo| image:: https://quay.io/repository/biocontainers/bioconductor-ringo/status :target: https://quay.io/repository/biocontainers/bioconductor-ringo .. _`bioconductor-ringo/tags`: https://quay.io/repository/biocontainers/bioconductor-ringo?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-ringo/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-ringo/README.html