recipe bioconductor-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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/Ringo.html

License

Artistic-2.0

Recipe

/bioconductor-ringo/meta.yaml

Links

biotools: ringo

package bioconductor-ringo

(downloads) docker_bioconductor-ringo

Versions

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

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-genefilter

>=1.64.0,<1.65.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-vsn

>=3.50.0,<3.51.0

Depends libgcc-ng

>=7.3.0

Depends libstdcxx-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-lattice

Depends r-matrix

Depends r-rcolorbrewer

Requirements

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>)