-
recipe
bioconductor-dmrseq¶ 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.
- Homepage
- License
MIT + file LICENSE
- Recipe
-
package
bioconductor-dmrseq¶ 
- Versions
1.2.1-0
- Depends bioconductor-annotationhub
>=2.14.0,<2.15.0
- Depends bioconductor-annotatr
>=1.8.0,<1.9.0
- Depends bioconductor-biocparallel
>=1.16.0,<1.17.0
- Depends bioconductor-bsseq
>=1.18.0,<1.19.0
- Depends bioconductor-bumphunter
>=1.24.0,<1.25.0
- Depends bioconductor-delayedmatrixstats
>=1.4.0,<1.5.0
- Depends bioconductor-genomeinfodb
>=1.18.0,<1.19.0
- Depends bioconductor-genomicranges
>=1.34.0,<1.35.0
- Depends bioconductor-iranges
>=2.16.0,<2.17.0
- Depends bioconductor-rtracklayer
>=1.42.0,<1.43.0
- Depends bioconductor-s4vectors
>=0.20.0,<0.21.0
- Depends r-base
>=3.5.1,<3.5.2.0a0
- Depends r-ggplot2
- Depends r-locfit
- Depends r-matrixstats
- Depends r-nlme
- Depends r-outliers
- Depends r-rcolorbrewer
- Requirements
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:
[](http://bioconda.github.io/recipes/bioconductor-dmrseq/README.html)