netSmooth

DOI: 10.18129/B9.bioc.netSmooth  

Network smoothing for scRNAseq

Bioconductor version: Release (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 gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

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)
LinkingTo
Suggests	knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
SystemRequirements
Enhances
URL	https://github.com/BIMSBbioinfo/netSmooth
BugReports	https://github.com/BIMSBbioinfo/netSmooth/issues
Depends On Me
Imports Me
Suggests Me	netDx
Links To Me
Build Report

Package Archives

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

Source Package	netSmooth_1.18.0.tar.gz
Windows Binary	netSmooth_1.18.0.zip
macOS Binary (x86_64)	netSmooth_1.18.0.tgz
macOS Binary (arm64)	netSmooth_1.18.0.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