recipe bioconductor-dmrscan

Detection of Differentially Methylated Regions

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-dmrscan/meta.yaml

This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.

package bioconductor-dmrscan

versions:

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.11.0-0, 

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.11.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends r-base:

>=4.4,<4.5.0a0

depends r-mass:

depends r-matrix:

depends r-mvtnorm:

depends r-rcpproll:

requirements:

additional platforms:

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-dmrscan

and update with::

   mamba update bioconductor-dmrscan

To create a new environment, run:

mamba create --name myenvname bioconductor-dmrscan

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-dmrscan:<tag>

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

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