netSmooth
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see netSmooth.
Network smoothing for scRNAseq
Bioconductor version: 3.11
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 "4.0") 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 |
Details
| biocViews | Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 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 | netDx |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | netSmooth_1.8.0.tar.gz |
| Windows Binary | netSmooth_1.8.0.zip |
| macOS 10.13 (High Sierra) | netSmooth_1.8.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |