recipe bioconductor-ringo

R Investigation of ChIP-chip Oligoarrays

Homepage:

https://bioconductor.org/packages/3.16/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:

1.62.0-0,  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, 

1.62.0-0,  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 >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-genefilter >=1.80.0,<1.81.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-vsn >=3.66.0,<3.67.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-lattice

• r-matrix

• r-rcolorbrewer

Required By:

• bioconductor-simbindprofiles

• bioconductor-cctutorial

• bioconductor-repitools

Installation

With an activated Bioconda channel (see 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>)

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