- recipe bioconductor-normalize450k
Preprocessing of Illumina Infinium 450K data
BSD_2_clause + file LICENSE
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¶
- depends bioconductor-biobase:
- depends bioconductor-illuminaio:
- depends r-base:
- depends r-quadprog:
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-normalize450k and update with:: mamba update bioconductor-normalize450k
To create a new environment, run:
mamba create --name myenvname bioconductor-normalize450k
myenvnamebeing 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-normalize450k:<tag> (see `bioconductor-normalize450k/tags`_ for valid values for ``<tag>``)