netSmooth
This is thereleased version of netSmooth; for the devel version, seenetSmooth.
Network smoothing for scRNAseq
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("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 appropriateBioconductor 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 |
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 |
See More
| Suggests | knitr,testthat,Rtsne,biomaRt,igraph,STRINGdb,NMI,pheatmap,ggplot2,BiocStyle,rmarkdown,BiocParallel,uwot |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation 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/ |
| Package Downloads Report | Download Stats |