recipe bioconductor-chromvar

Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/chromVAR.html

License

MIT + file LICENSE

Recipe

/bioconductor-chromvar/meta.yaml

Links

biotools: chromvar

package bioconductor-chromvar

Versions

1.6.0-1, 1.4.1-0, 1.4.0-1, 1.4.0-0, 1.2.0-0

Depends

• bioconductor-biocgenerics >=0.30.0,<0.31.0

• bioconductor-biocparallel >=1.18.0,<1.19.0

• bioconductor-biostrings >=2.52.0,<2.53.0

• bioconductor-bsgenome >=1.52.0,<1.53.0

• bioconductor-genomeinfodb >=1.20.0,<1.21.0

• bioconductor-genomicranges >=1.36.0,<1.37.0

• bioconductor-iranges >=2.18.0,<2.19.0

• bioconductor-rsamtools >=2.0.0,<2.1.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• bioconductor-summarizedexperiment >=1.14.0,<1.15.0

• bioconductor-tfbstools >=1.22.0,<1.23.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• r-dt

• r-ggplot2

• r-matrix

• r-miniui

• r-nabor

• r-plotly

• r-rcolorbrewer

• r-rcpp

• r-rcpparmadillo

• r-rtsne

• r-shiny

Required By

• stream_atac

Installation

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

conda install bioconductor-chromvar

and update with:

conda update bioconductor-chromvar

or use the docker container:

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

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