recipe bioconductor-compartmap

Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq

Homepage

https://bioconductor.org/packages/3.13/bioc/html/compartmap.html

License

GPL-3 + file LICENSE

Recipe

/bioconductor-compartmap/meta.yaml

Compartmap performs direct inference of higher-order chromatin from scRNA-seq and scATAC-seq. This package implements a James-Stein estimator for computing single-cell level higher-order chromatin domains. Further, we utilize random matrix theory as a method to de-noise correlation matrices to achieve a similar "plaid-like" patterning as observed in Hi-C and scHi-C data.

package bioconductor-compartmap

Versions

1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.2-0

Depends

• bioconductor-biocsingular >=1.8.0,<1.9.0

• bioconductor-delayedarray >=0.18.0,<0.19.0

• bioconductor-delayedmatrixstats >=1.14.0,<1.15.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-hdf5array >=1.20.0,<1.21.0

• bioconductor-raggedexperiment >=1.16.0,<1.17.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

• r-matrix

• r-reshape2

• r-rmtstat

• r-scales

Required By

Installation

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

conda install bioconductor-compartmap

and update with:

conda update bioconductor-compartmap

or use the docker container:

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

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

Download stats

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-compartmap/README.html)