recipe bioconductor-methylaid

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/MethylAid.html

License:

GPL (>= 2)

Recipe:

/bioconductor-methylaid/meta.yaml

A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

package bioconductor-methylaid

Versions:

1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-minfi >=1.44.0,<1.45.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-gridbase

• r-hexbin

• r-matrixstats

• r-rcolorbrewer

• r-shiny

Required By:

• bioconductor-methylaiddata

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-methylaid

and update with:

conda update bioconductor-methylaid

or use the docker container:

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

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

Download stats

Link to this page

Render an badge with the following MarkDown:

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