netSmooth
Network smoothing for scRNAseq
Bioconductor version: Release (3.19)
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 "4.4") 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 | 1.24.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 | netDx |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | netSmooth_1.24.0.tar.gz |
Windows Binary | netSmooth_1.24.0.zip |
macOS Binary (x86_64) | netSmooth_1.24.0.tgz |
macOS Binary (arm64) | netSmooth_1.24.0.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 |