netSmooth

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

Network smoothing for scRNAseq

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DOI: 10.18129/B9.bioc.netSmooth

Bioconductor version: Release (3.22)

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 "4.5") 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 1.30.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 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

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Package Archives

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

Source Package netSmooth_1.30.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) netSmooth_1.30.0.tgz

macOS Binary (arm64) netSmooth_1.30.0.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/

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