recipe bioconductor-methrix

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Homepage

https://bioconductor.org/packages/3.14/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

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

Depends

• bioconductor-bsgenome >=1.62.0,<1.63.0

• bioconductor-delayedarray >=0.20.0,<0.21.0

• bioconductor-delayedmatrixstats >=1.16.0,<1.17.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-hdf5array >=1.22.0,<1.23.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-data.table >=1.12.4

• r-ggplot2

• r-matrixstats

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-methrix

and update with:

conda update bioconductor-methrix

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-methrix:<tag>

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

Download stats

Link to this page

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