netSmooth

This is the released version of netSmooth; for the devel version, see netSmooth.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Network smoothing for scRNAseq

Bioconductor version: Release (3.23)

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 gmail.com>

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

Jonathan Ronen, Altuna Akalin. netSmooth: Network smoothing for scRNAseq. doi:10.18129/B9.bioc.netSmooth, R package version 1.32.0, https://bioconductor.org/packages/netSmooth.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("netSmooth")

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

Documentation

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

browseVignettes("netSmooth")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 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)
System Requirements
URL	https://github.com/BIMSBbioinfo/netSmooth
Bug Reports	https://github.com/BIMSBbioinfo/netSmooth/issues

Suggests	knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
Linking To
Enhances
Depends On Me
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	netSmooth_1.32.0.tar.gz
Windows Binary (x86_64)	netSmooth_1.32.0.zip
macOS Binary (big-sur-x86_64)	netSmooth_1.32.0.tgz
macOS Binary (sonoma-arm64)	netSmooth_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/netSmooth
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/netSmooth
Package Short Url	https://bioconductor.org/packages/netSmooth/
Package Downloads Report	Download Stats