recipe bioconductor-netsmooth

Network smoothing for scRNAseq

Homepage

https://bioconductor.org/packages/3.12/bioc/html/netSmooth.html

License

GPL-3

Recipe

/bioconductor-netsmooth/meta.yaml

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.

package bioconductor-netsmooth

Versions

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

Depends

• bioconductor-clusterexperiment >=2.10.0,<2.11.0

• bioconductor-delayedarray >=0.16.0,<0.17.0

• bioconductor-hdf5array >=1.18.0,<1.19.0

• bioconductor-scater >=1.18.0,<1.19.0

• bioconductor-singlecellexperiment >=1.12.0,<1.13.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• r-base >=4.0,<4.1.0a0

• r-cluster

• r-data.table

• r-entropy

• r-matrix

Required By

• bioconductor-netdx

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>)

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-netsmooth/README.html)