recipe bioconductor-gothic

Binomial test for Hi-C data analysis

Homepage

https://bioconductor.org/packages/3.11/bioc/html/GOTHiC.html

License

GPL-3

Recipe

/bioconductor-gothic/meta.yaml

Links

biotools: gothic, doi: 10.1101/gr.185272.114

This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.

package bioconductor-gothic

Versions

1.24.0-0,  1.22.0-0,  1.20.6-0,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0

Depends

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-shortread >=1.46.0,<1.47.0

• r-base >=4.0,<4.1.0a0

• r-biocmanager

• r-data.table

• r-ggplot2

Required By

Installation

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

conda install bioconductor-gothic

and update with:

conda update bioconductor-gothic

or use the docker container:

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

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

Link to this page

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