recipe bioconductor-normalize450k

Preprocessing of Illumina Infinium 450K data

Homepage:

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

(downloads) docker_bioconductor-normalize450k

Versions:
1.38.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0, 

1.38.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-0,  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:

  • on bioconductor-biobase >=2.70.0,<2.71.0

  • on bioconductor-illuminaio >=0.52.0,<0.53.0

  • on r-base >=4.5,<4.6.0a0

  • on r-quadprog

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-normalize450k

to add into an existing workspace instead, run:

pixi add bioconductor-normalize450k

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-normalize450k

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-normalize450k

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-normalize450k:<tag>

(see bioconductor-normalize450k/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.

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