recipe bioconductor-netsmooth

Network smoothing for scRNAseq

Homepage:

https://bioconductor.org/packages/3.18/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:

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0, 

1.22.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  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:

>=2.22.0,<2.23.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-scater:

>=1.30.0,<1.31.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-data.table:

depends r-entropy:

depends r-matrix:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-netsmooth

and update with::

   mamba update bioconductor-netsmooth

To create a new environment, run:

mamba create --name myenvname bioconductor-netsmooth

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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Link to this page

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