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Network smoothing for scRNAseq

Bioconductor version: Release (3.19)

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 "4.4") and enter:

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


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:

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


biocViews Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.5), scater(>= 1.15.11), clusterExperiment(>= 2.1.6)
Imports entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods, DelayedArray, HDF5Array(>= 1.15.13)
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Suggests knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
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Follow Installation instructions to use this package in your R session.

Source Package netSmooth_1.24.0.tar.gz
Windows Binary
macOS Binary (x86_64) netSmooth_1.24.0.tgz
macOS Binary (arm64) netSmooth_1.24.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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