recipe bioconductor-beclear

Correction of batch effects in DNA methylation data

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-beclear/meta.yaml

Links:

biotools: beclear, doi: 10.1371/journal.pone.0159921

Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

package bioconductor-beclear

versions:

2.22.0-0,  2.18.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.10.0-2,  2.10.0-1,  2.10.0-0, 

2.22.0-0,  2.18.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.14.0-0,  2.10.0-2,  2.10.0-1,  2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.4.0-0,  2.2.0-0,  2.0.0-1,  2.0.0-0,  1.14.0-0,  1.12.1-0,  1.10.0-0,  1.8.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-abind:

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

>=1.11.8

depends r-dixontest:

depends r-futile.logger:

depends r-ids:

depends r-matrix:

depends r-rcpp:

depends r-rdpack:

requirements:

additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-beclear

and update with::

   mamba update bioconductor-beclear

To create a new environment, run:

mamba create --name myenvname bioconductor-beclear

with myenvname being 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-beclear:<tag>

(see `bioconductor-beclear/tags`_ for valid values for ``<tag>``)

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