Package Recipe 'bioconductor-skewr'

recipe bioconductor-skewr

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

Homepage:: https://bioconductor.org/packages/3.20/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:

1.42.0-0, 1.38.0-0, 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,

1.42.0-0, 1.38.0-0, 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:

on bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0
on bioconductor-methylumi >=2.56.0,<2.57.0
on bioconductor-minfi >=1.56.0,<1.57.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-watermelon >=2.16.0,<2.17.0
on r-base >=4.5,<4.6.0a0
on r-mixsmsn
on r-rcolorbrewer

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-skewr

to add into an existing workspace instead, run:

pixi add bioconductor-skewr

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-skewr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-skewr

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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-skewr/README.html)