recipe bioconductor-dyebias

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

Homepage

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

1.50.0-0,  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 >=2.50.0,<2.51.0

• bioconductor-marray >=1.68.0,<1.69.0

• r-base >=4.0,<4.1.0a0

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>)

Link to this page

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