DOI: 10.18129/B9.bioc.netSmooth    

This is the development version of netSmooth; to use it, please install the devel version of Bioconductor.

Network smoothing for scRNAseq

Bioconductor version: Development (3.10)

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.

Author: Jonathan Ronen [aut, cre], Altuna Akalin [aut]

Maintainer: Jonathan Ronen <yablee at>

Citation (from within R, enter citation("netSmooth")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Generation of PPI graph
HTML R Script netSmooth example
PDF   Reference Manual


biocViews Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.5.1
In Bioconductor since BioC 3.7 (R-3.5) (1.5 years)
License GPL-3
Depends R (>= 3.5), scater(>= 1.9.20), clusterExperiment(>= 2.1.6)
Imports entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array
Suggests knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
Depends On Me
Imports Me
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package netSmooth_1.5.1.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.11 (El Capitan) netSmooth_1.5.1.tgz
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