recipe bioconductor-methylimp2

Missing value estimation of DNA methylation data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/methyLImp2.html

License:

GPL-3

Recipe:

/bioconductor-methylimp2/meta.yaml

This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.

package bioconductor-methylimp2

(downloads) docker_bioconductor-methylimp2

Versions:

1.6.0-0,  1.2.0-0

Depends:

  • on bioconductor-biocparallel >=1.44.0,<1.45.0

  • on bioconductor-champdata >=2.42.0,<2.43.0

  • on bioconductor-summarizedexperiment >=1.40.0,<1.41.0

  • on r-base >=4.5,<4.6.0a0

  • on r-corpcor

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-methylimp2

to add into an existing workspace instead, run:

pixi add bioconductor-methylimp2

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-methylimp2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-methylimp2

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-methylimp2:<tag>

(see bioconductor-methylimp2/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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Render an install-with-bioconda badge with the following MarkDown:

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