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Bioconductor - netSmooth

netSmooth

This is the released version of netSmooth; for the devel version, see netSmooth.

Network smoothing for scRNAseq

Bioconductor version: Release (3.21)

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 (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 appropriate Bioconductor release.

Documentation

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

browseVignettes("netSmooth")
Details biocViews Clustering, DimensionReduction, GeneExpression, GraphAndNetwork, Network, Normalization, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics Version 1.28.0 In Bioconductor since BioC 3.7 (R-3.5) (7 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

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

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