recipe bioconductor-somnibus

Smooth modeling of bisulfite sequencing

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SOMNiBUS.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-somnibus/meta.yaml

This package aims to analyse count-based methylation data on predefined genomic regions, such as those obtained by targeted sequencing, and thus to identify differentially methylated regions (DMRs) that are associated with phenotypes or traits. The method is built a rich flexible model that allows for the effects, on the methylation levels, of multiple covariates to vary smoothly along genomic regions. At the same time, this method also allows for sequencing errors and can adjust for variability in cell type mixture.

package bioconductor-somnibus

versions:

1.10.0-0,  1.7.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-annotatr:

>=1.28.0,<1.29.0

depends bioconductor-bsseq:

>=1.38.0,<1.39.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

depends r-data.table:

depends r-ggplot2:

depends r-matrix:

depends r-mgcv:

depends r-reshape2:

depends r-tidyr:

depends r-vgam:

depends r-yaml:

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-somnibus

and update with::

   mamba update bioconductor-somnibus

To create a new environment, run:

mamba create --name myenvname bioconductor-somnibus

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-somnibus:<tag>

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

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