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netSmooth

This is the development version of netSmooth; for the stable release version, see netSmooth.

Network smoothing for scRNAseq


Bioconductor version: Development (3.20)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.25.0
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)
System Requirements
URL https://github.com/BIMSBbioinfo/netSmooth
Bug Reports https://github.com/BIMSBbioinfo/netSmooth/issues
See More
Suggests knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
Linking To
Enhances
Depends On Me
Imports Me
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Build Report Build Report

Package Archives

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

Source Package netSmooth_1.25.0.tar.gz
Windows Binary netSmooth_1.25.0.zip
macOS Binary (x86_64) netSmooth_1.25.0.tgz
macOS Binary (arm64) netSmooth_1.25.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/netSmooth
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/netSmooth
Bioc Package Browser https://code.bioconductor.org/browse/netSmooth/
Package Short Url https://bioconductor.org/packages/netSmooth/
Package Downloads Report Download Stats