- recipe bioconductor-compartmap
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq
- Homepage
https://bioconductor.org/packages/3.14/bioc/html/compartmap.html
- License
GPL-3 + file LICENSE
- Recipe
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
1.12.0-0
,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
>=1.10.0,<1.11.0
bioconductor-delayedarray
>=0.20.0,<0.21.0
bioconductor-delayedmatrixstats
>=1.16.0,<1.17.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-hdf5array
>=1.22.0,<1.23.0
bioconductor-raggedexperiment
>=1.18.0,<1.19.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
r-base
>=4.1,<4.2.0a0
- 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:
[](http://bioconda.github.io/recipes/bioconductor-compartmap/README.html)