recipe bioconductor-dyebias

The GASSCO method for correcting for slide-dependent gene-specific dye bias

Homepage

https://bioconductor.org/packages/3.14/bioc/html/dyebias.html

License

GPL-3

Recipe

/bioconductor-dyebias/meta.yaml

Links

biotools: dyebias

Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21)

package bioconductor-dyebias

Versions

1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.42.0-0,  1.40.0-0, 

1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-0,  1.44.0-1,  1.42.0-0,  1.40.0-0,  1.38.0-0

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-marray >=1.72.0,<1.73.0

• r-base >=4.1,<4.2.0a0

Required By

Installation

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

conda install bioconductor-dyebias

and update with:

conda update bioconductor-dyebias

or use the docker container:

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

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

Download stats

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-dyebias/README.html)