recipe bioconductor-dyebias

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

Homepage:

https://bioconductor.org/packages/3.18/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

(downloads) docker_bioconductor-dyebias

versions:
1.62.0-0,  1.60.0-0,  1.58.0-0,  1.54.0-0,  1.52.0-0,  1.50.0-1,  1.50.0-0,  1.48.0-0,  1.46.0-0, 

1.62.0-0,  1.60.0-0,  1.58.0-0,  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:

>=2.62.0,<2.63.0

depends bioconductor-marray:

>=1.80.0,<1.81.0

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-dyebias

and update with::

   mamba update bioconductor-dyebias

To create a new environment, run:

mamba create --name myenvname bioconductor-dyebias

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, 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 install-with-bioconda 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)