recipe bioconductor-skewr

Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/skewr.html

License:

GPL-2

Recipe:

/bioconductor-skewr/meta.yaml

The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of 'tick' marks located above the x-axis.

package bioconductor-skewr

versions:

1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0, 

1.34.0-0,  1.32.0-0,  1.30.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.14.0-0

depends bioconductor-illuminahumanmethylation450kmanifest:

>=0.4.0,<0.5.0

depends bioconductor-methylumi:

>=2.48.0,<2.49.0

depends bioconductor-minfi:

>=1.48.0,<1.49.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-watermelon:

>=2.8.0,<2.9.0

depends r-base:

>=4.3,<4.4.0a0

depends r-mixsmsn:

depends r-rcolorbrewer:

requirements:

additional platforms:

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-skewr

and update with::

   mamba update bioconductor-skewr

To create a new environment, run:

mamba create --name myenvname bioconductor-skewr

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-skewr:<tag>

(see `bioconductor-skewr/tags`_ for valid values for ``<tag>``)

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