--------- \[!\[DOI\](https://zenodo.org/badge/DOI/10.5281/zenodo.1119064.svg)\](https://doi.org/10.5281/zenodo.1119064) \[!\[Build Status\](http://bioconductor.org/shields/build/devel/bioc/netSmooth.svg)\](https://travis-ci.org/BIMSBbioinfo/netSmooth) \[!\[codecov\](https://codecov.io/gh/BIMSBbioinfo/netSmooth/branch/master/graph/badge.svg)\](https://codecov.io/gh/BIMSBbioinfo/netSmooth) \[!\[BioC\_years\](http://www.bioconductor.org/shields/years-in-bioc/netSmooth.svg)\](http://www.bioconductor.org/packages/release/bioc/html/netSmooth.html) \*\*\_netSmooth\_: A Network smoothing based method for single cell RNA-seq\*\* ----- \_netSmooth\_ is an R package for network smoothing of single cell RNA sequencing data. Using gene interaction networks such as protein- protein interactions as priors for gene co-expression, \_netsmooth\_ improves cell type identification from noisy, sparse scRNA-seq data. The smoothing method is suitable for other gene-based omics data sets such as proteomics, copy-number variation, etc. The algorithm uses a network-diffusion based approach which takes in a network (such as PPI network) and gene-expression matrix. The gene expression values in the matrix are smoothed using the interaction information in the network. The network-smoothing parameter is optimized using a robust clustering approach. For a detailed exposition, check out \[our paper on F1000Research\](https://f1000research.com/articles/7-8/v2). ### Installation \_netSmooth\_ is available via Bioconductor: if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("netSmooth") Alternatively, using \`devtools\`: library(devtools) install\_github("BIMSBbioinfo/netSmooth") ### Usage For detailed usage information see \[the vignette\](http://htmlpreview.github.io/?https://github.com/BIMSBbioinfo/netSmooth/blob/master/vignettes/netSmoothIntro.html). In addition, the R package has full function documentation with examples. ### How to cite Please cite the \_netSmooth\_ paper: > Ronen J and Akalin A. \_netSmooth\_: Network-smoothing based imputation for single cell RNA-seq \[version 2; referees: 2 approved\]. F1000Research 2018, 7:8 (doi: 10.12688/f1000research.13511.2) ### License \_netSmooth\_ is available under a GPLv3 license. ### Contributing Fork and send a pull request. Or just e-mail us. ------------------------- @jonathanronen, BIMSBbioinfo, 2017
