recipe bioconductor-biseq

Processing and analyzing bisulfite sequencing data

Homepage

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

License

LGPL-3

Recipe

/bioconductor-biseq/meta.yaml

Links

biotools: biseq, doi: 10.1093/bib/bbv095

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

package bioconductor-biseq

Versions

1.28.0-0,  1.26.0-0,  1.24.0-1,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-globaltest >=5.42.0,<5.43.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• r-betareg

• r-formula

• r-lokern

Required By

• bioconductor-rrbsdata

• bioconductor-m3d

Installation

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

conda install bioconductor-biseq

and update with:

conda update bioconductor-biseq

or use the docker container:

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

(see bioconductor-biseq/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-biseq/README.html)