netSmooth

DOI: 10.18129/B9.bioc.netSmooth    

Network smoothing for scRNAseq

Bioconductor version: Release (3.7)

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:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("netSmooth")

Documentation

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 1.0.1
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
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package netSmooth_1.0.1.tar.gz
Windows Binary netSmooth_1.0.1.zip
Mac OS X 10.11 (El Capitan) netSmooth_1.0.1.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
Old Source Packages for BioC 3.7 Source Archive

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