recipe bioconductor-netsmooth

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.

Homepage

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

License

GPL-3

Recipe

/bioconductor-netsmooth/meta.yaml

package bioconductor-netsmooth

(downloads) docker_bioconductor-netsmooth

Versions

1.2.0-1, 1.2.0-0

Depends bioconductor-clusterexperiment

>=2.2.0,<2.3.0

Depends bioconductor-scater

>=1.10.0,<1.11.0

Depends bioconductor-singlecellexperiment

>=1.4.0,<1.5.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-cluster

Depends r-data.table

Depends r-entropy

Depends r-matrix

Requirements

Installation

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

conda install bioconductor-netsmooth

and update with:

conda update bioconductor-netsmooth

or use the docker container:

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

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