recipe bioconductor-dmrseq

Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Homepage

https://bioconductor.org/packages/3.11/bioc/html/dmrseq.html

License

MIT + file LICENSE

Recipe

/bioconductor-dmrseq/meta.yaml

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.

package bioconductor-dmrseq

Versions

1.8.0-0,  1.6.0-0,  1.4.9-0,  1.2.1-0

Depends

• bioconductor-annotationhub >=2.20.0,<2.21.0

• bioconductor-annotatr >=1.14.0,<1.15.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-bsseq >=1.24.0,<1.25.0

• bioconductor-bumphunter >=1.30.0,<1.31.0

• bioconductor-delayedmatrixstats >=1.10.0,<1.11.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-locfit

• r-matrixstats

• r-nlme

• r-outliers

• r-rcolorbrewer

Required By

• bioconductor-biscuiteer

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-dmrseq

and update with:

conda update bioconductor-dmrseq

or use the docker container:

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

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

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-dmrseq/README.html)