:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-netsmooth' .. highlight: bash bioconductor-netsmooth ====================== .. conda:recipe:: bioconductor-netsmooth :replaces_section_title: :noindex: 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. .. conda:package:: bioconductor-netsmooth |downloads_bioconductor-netsmooth| |docker_bioconductor-netsmooth| :versions: .. raw:: html
1.22.0-01.20.0-01.18.0-01.14.0-01.12.0-01.10.0-11.10.0-01.8.0-01.6.0-0 ``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`` .. raw:: html
: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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `bioconductor-netsmooth/tags`_ for valid values for ````) .. |downloads_bioconductor-netsmooth| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-netsmooth.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-netsmooth :alt: (downloads) .. |docker_bioconductor-netsmooth| image:: https://quay.io/repository/biocontainers/bioconductor-netsmooth/status :target: https://quay.io/repository/biocontainers/bioconductor-netsmooth .. _`bioconductor-netsmooth/tags`: https://quay.io/repository/biocontainers/bioconductor-netsmooth?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-netsmooth/README.html