recipe bioconductor-dmrforpairs

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-dmrforpairs/meta.yaml

DMRforPairs (formerly DMR2+) allows researchers to compare n>=2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

package bioconductor-dmrforpairs

(downloads) docker_bioconductor-dmrforpairs

Versions:
1.35.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1, 

1.35.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.18.0-0

Depends:

  • on bioconductor-genomicranges >=1.52.0,<1.53.0

  • on bioconductor-gviz >=1.44.0,<1.45.0

  • on r-base >=4.3,<4.4.0a0

  • on r-r2html >=2.2.1

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-dmrforpairs

to add into an existing workspace instead, run:

pixi add bioconductor-dmrforpairs

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-dmrforpairs

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-dmrforpairs

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-dmrforpairs:<tag>

(see bioconductor-dmrforpairs/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.

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