Package Recipe 'bioconductor-chromvar'

recipe bioconductor-chromvar

Chromatin Variation Across Regions

Homepage: https://bioconductor.org/packages/3.13/bioc/html/chromVAR.html
License: MIT + file LICENSE
Recipe: /bioconductor-chromvar/meta.yaml
Links: biotools: 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.

package bioconductor-chromvar¶

Versions

1.14.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.4.1-0, 1.4.0-1, 1.4.0-0,

1.14.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.4.1-0, 1.4.0-1, 1.4.0-0, 1.2.0-0

Depends

bioconductor-biocgenerics >=0.38.0,<0.39.0
bioconductor-biocparallel >=1.26.0,<1.27.0
bioconductor-biostrings >=2.60.0,<2.61.0
bioconductor-bsgenome >=1.60.0,<1.61.0
bioconductor-genomeinfodb >=1.28.0,<1.29.0
bioconductor-genomicranges >=1.44.0,<1.45.0
bioconductor-iranges >=2.26.0,<2.27.0
bioconductor-rsamtools >=2.8.0,<2.9.0
bioconductor-s4vectors >=0.30.0,<0.31.0
bioconductor-summarizedexperiment >=1.22.0,<1.23.0
bioconductor-tfbstools >=1.30.0,<1.31.0
libblas >=3.8.0,<4.0a0
libgcc-ng >=9.3.0
liblapack >=3.8.0,<4.0a0
libstdcxx-ng >=9.3.0
r-base >=4.1,<4.2.0a0
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)