recipe bioconductor-intad

Search for correlation between epigenetic signals and gene expression in TADs

Homepage

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

License

GPL (>=2)

Recipe

/bioconductor-intad/meta.yaml

The package is focused on the detection of correlation between expressed genes and selected epigenomic signals i.e. enhancers obtained from ChIP-seq data within topologically associated domains (TADs). Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.

package bioconductor-intad

Versions

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.1-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-multiassayexperiment >=1.14.0,<1.15.0

• bioconductor-qvalue >=2.20.0,<2.21.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-ggpubr

• r-mclust

Required By

Installation

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

conda install bioconductor-intad

and update with:

conda update bioconductor-intad

or use the docker container:

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

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