recipe bioconductor-methrix

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/methrix.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-methrix/meta.yaml

Bedgraph files generated by Bisulfite pipelines often come in various flavors. Critical downstream step requires summarization of these files into methylation/coverage matrices. This step of data aggregation is done by Methrix, including many other useful downstream functions.

package bioconductor-methrix

versions:

1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.07-0,  1.4.0-0,  1.2.05-0,  1.0.0-0

depends bioconductor-bsgenome:

>=1.68.0,<1.69.0

depends bioconductor-delayedarray:

>=0.26.0,<0.27.0

depends bioconductor-delayedmatrixstats:

>=1.22.0,<1.23.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-hdf5array:

>=1.28.0,<1.29.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

>=1.12.4

depends r-ggplot2:

depends r-matrixstats:

requirements:

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-methrix

and update with::

   mamba update bioconductor-methrix

To create a new environment, run:

mamba create --name myenvname bioconductor-methrix

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-methrix:<tag>

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

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