recipe bioconductor-normalize450k

Preprocessing of Illumina Infinium 450K data

Homepage

https://bioconductor.org/packages/3.14/bioc/html/normalize450K.html

License

BSD_2_clause + file LICENSE

Recipe

/bioconductor-normalize450k/meta.yaml

Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.

package bioconductor-normalize450k

Versions

1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0

Depends

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-illuminaio >=0.36.0,<0.37.0

• r-base >=4.1,<4.2.0a0

• r-quadprog

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-normalize450k

and update with:

conda update bioconductor-normalize450k

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-normalize450k:<tag>

(see bioconductor-normalize450k/tags for valid values for <tag>)

Download stats

Link to this page

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