DOI: 10.18129/B9.bioc.netSmooth  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see netSmooth.

Network smoothing for scRNAseq

Bioconductor version: 3.16

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")):


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


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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 1.18.0
In Bioconductor since BioC 3.7 (R-3.5) (5 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)
Suggests knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
Depends On Me
Imports Me
Suggests Me netDx
Links To Me
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