recipe bioconductor-hicdcplus

Hi-C Direct Caller Plus

Homepage:

https://bioconductor.org/packages/3.16/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:

1.6.0-0,  1.2.1-1,  1.2.1-0,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicinteractions >=1.32.0,<1.33.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-interactionset >=1.26.0,<1.27.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• 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 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

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