recipe bioconductor-chromvar

Chromatin Variation Across Regions

Homepage

https://bioconductor.org/packages/3.14/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

1.16.0-1,  1.16.0-0,  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, 

1.16.0-1,  1.16.0-0,  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 >=0.40.0,<0.41.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-biostrings >=2.62.0,<2.63.0

• bioconductor-bsgenome >=1.62.0,<1.63.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rsamtools >=2.10.0,<2.11.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• bioconductor-tfbstools >=1.32.0,<1.33.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=10.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=10.3.0

• 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>)

Download stats

Link to this page

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