recipe bioconductor-ringo

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: 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.

package bioconductor-ringo

versions:

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, 

1.66.0-0,  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

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:

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-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:<tag>

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

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