Package Recipe 'bioconductor-somnibus'

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:

1.18.0-0, 1.10.0-0, 1.7.0-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-annotatr >=1.36.0,<1.37.0
on bioconductor-bsseq >=1.46.0,<1.47.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on r-base >=4.5,<4.6.0a0
on r-biocmanager
on r-data.table
on r-ggplot2
on r-matrix
on r-mgcv
on r-reshape2
on r-tidyr
on r-vgam
on r-yaml

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-somnibus

to add into an existing workspace instead, run:

pixi add bioconductor-somnibus

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-somnibus

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-somnibus

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-somnibus:<tag>

(see bioconductor-somnibus/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.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-somnibus/README.html)