recipe bioconductor-diffbind

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

Homepage

https://bioconductor.org/packages/3.8/bioc/html/DiffBind.html

License

Artistic-2.0

Recipe

/bioconductor-diffbind/meta.yaml

Links

biotools: diffbind

package bioconductor-diffbind

Versions

2.10.0-1, 2.10.0-0, 2.8.0-0, 2.6.6-0, 2.6.5-0, 2.6.0-0, 2.4.8-16, 2.2.12-1, 2.2.12-0, 2.0.9-3, 2.0.9-2, 1.16.3-0

Depends

• bioconductor-biocparallel >=1.16.0,<1.17.0

• bioconductor-deseq2 >=1.22.0,<1.23.0

• bioconductor-edger >=3.24.0,<3.25.0

• bioconductor-genomicalignments >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-limma >=3.38.0,<3.39.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• bioconductor-systempiper >=1.16.0,<1.17.0

• bioconductor-zlibbioc >=1.28.0,<1.29.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-amap

• r-base >=3.5.1,<3.5.2.0a0

• r-dplyr

• r-ggplot2

• r-ggrepel

• r-gplots

• r-lattice

• r-locfit

• r-rcolorbrewer

• r-rcpp

Required By

• bioconductor-mmdiff

• bioconductor-vulcan

• bioconductor-chipqc

Installation

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

conda install bioconductor-diffbind

and update with:

conda update bioconductor-diffbind

or use the docker container:

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

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