recipe bioconductor-hicdcplus

Hi-C Direct Caller Plus

Homepage

https://bioconductor.org/packages/3.14/bioc/html/HiCDCPlus.html

License

GPL-3

Recipe

/bioconductor-hicdcplus/meta.yaml

Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies. HiC-DC+ estimates significant interactions in a Hi-C or HiChIP experiment directly from the raw contact matrix for each chromosome up to a specified genomic distance, binned by uniform genomic intervals or restriction enzyme fragments, by training a background model to account for random polymer ligation and systematic sources of read count variation.

package bioconductor-hicdcplus

Versions

1.2.0-0,  1.0.0-0

Depends

• bioconductor-biostrings >=2.62.0,<2.63.0

• bioconductor-bsgenome >=1.62.0,<1.63.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicinteractions >=1.28.0,<1.29.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-interactionset >=1.22.0,<1.23.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.4.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.4.0

• r-base >=4.1,<4.2.0a0

• r-bbmle

• r-data.table

• r-dplyr

• r-mass

• r-pscl

• r-r.utils

• r-rcpp

• r-rlang

• r-tibble

• r-tidyr

Required By

Installation

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

conda install bioconductor-hicdcplus

and update with:

conda update bioconductor-hicdcplus

or use the docker container:

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

(see bioconductor-hicdcplus/tags for valid values for <tag>)

Download stats

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-hicdcplus/README.html)