recipe bioconductor-dmrscan

Detection of Differentially Methylated Regions

Homepage:

https://bioconductor.org/packages/3.16/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:

1.20.0-0,  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 >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• r-base >=4.2,<4.3.0a0

• r-mass

• r-matrix

• r-mvtnorm

• r-rcpproll

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-dmrscan

and update with:

conda update bioconductor-dmrscan

or use the docker container:

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

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

Download stats

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