recipe bioconductor-diffhic

Differential Analyis of Hi-C Data

Homepage

https://bioconductor.org/packages/3.10/bioc/html/diffHic.html

License

GPL-3

Recipe

/bioconductor-diffhic/meta.yaml

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.

package bioconductor-diffhic

Versions

1.18.0-0, 1.16.0-1, 1.14.0-0

Depends

• bioconductor-biocgenerics >=0.32.0,<0.33.0

• bioconductor-biostrings >=2.54.0,<2.55.0

• bioconductor-bsgenome >=1.54.0,<1.55.0

• bioconductor-csaw >=1.20.0,<1.21.0

• bioconductor-edger >=3.28.0,<3.29.0

• bioconductor-genomeinfodb >=1.22.0,<1.23.0

• bioconductor-genomicranges >=1.38.0,<1.39.0

• bioconductor-interactionset >=1.14.0,<1.15.0

• bioconductor-iranges >=2.20.0,<2.21.0

• bioconductor-limma >=3.42.0,<3.43.0

• bioconductor-rhdf5 >=2.30.0,<2.31.0

• bioconductor-rhtslib >=1.18.0,<1.19.0

• bioconductor-rsamtools >=2.2.0,<2.3.0

• bioconductor-rtracklayer >=1.46.0,<1.47.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• bioconductor-summarizedexperiment >=1.16.0,<1.17.0

• bioconductor-zlibbioc >=1.32.0,<1.33.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• 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)