recipe bioconductor-ringo

R Investigation of ChIP-chip Oligoarrays

Homepage

https://bioconductor.org/packages/3.12/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

1.54.0-0,  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, 

1.54.0-0,  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 >=2.50.0,<2.51.0

• bioconductor-biocgenerics >=0.36.0,<0.37.0

• bioconductor-genefilter >=1.72.0,<1.73.0

• bioconductor-limma >=3.46.0,<3.47.0

• bioconductor-vsn >=3.58.0,<3.59.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=7.5.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=7.5.0

• r-base >=4.0,<4.1.0a0

• r-lattice

• r-matrix

• r-rcolorbrewer

Required By

• bioconductor-repitools

• bioconductor-simbindprofiles

• bioconductor-cctutorial

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-ringo

and update with:

conda update bioconductor-ringo

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-ringo:<tag>

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

Link to this page

Render an 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)