netSmooth

DOI: 10.18129/B9.bioc.netSmooth    

Network smoothing for scRNAseq

Bioconductor version: Release (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("netSmooth", version = "3.8")

Documentation

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

browseVignettes("netSmooth")

 

HTML R Script netSmooth example
HTML R Script netSmooth example
PDF   Reference Manual

Details

biocViews Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.2.0
License GPL-3
Depends R (>= 3.5), scater(>= 1.7.11), clusterExperiment(>= 1.99.1)
Imports entropy, SummarizedExperiment, SingleCellExperiment, Matrix, cluster, data.table, stats, methods
LinkingTo
Suggests knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel
SystemRequirements
Enhances
URL https://github.com/BIMSBbioinfo/netSmooth
BugReports https://github.com/BIMSBbioinfo/netSmooth/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package netSmooth_1.2.0.tar.gz
Windows Binary netSmooth_1.2.0.zip
Mac OS X 10.11 (El Capitan) netSmooth_1.2.0.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 http://bioconductor.org/packages/netSmooth/
Package Downloads Report Download Stats

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