recipe bioconductor-diffhic

Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.

Homepage

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

License

GPL-3

Recipe

/bioconductor-diffhic/meta.yaml

package bioconductor-diffhic

Versions

1.14.0-0

Depends

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-bsgenome >=1.50.0,<1.51.0

• bioconductor-csaw >=1.16.0,<1.17.0

• bioconductor-edger >=3.24.0,<3.25.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-interactionset >=1.10.0,<1.11.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-limma >=3.38.0,<3.39.0

• bioconductor-rhdf5 >=2.26.0,<2.27.0

• bioconductor-rhtslib >=1.14.0,<1.15.0

• bioconductor-rsamtools >=1.34.0,<1.35.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-summarizedexperiment >=1.12.0,<1.13.0

• bioconductor-zlibbioc >=1.28.0,<1.29.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.5.1,<3.5.2.0a0

• r-locfit

• r-rcpp

Required By

Installation

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

conda install bioconductor-diffhic

and update with:

conda update bioconductor-diffhic

or use the docker container:

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

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