netSmooth
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Science Score: 33.0%
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✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
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2 of 12 committers (16.7%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (13.6%) to scientific vocabulary
Keywords
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Repository
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Basic Info
Statistics
- Stars: 28
- Watchers: 14
- Forks: 6
- Open Issues: 5
- Releases: 0
Topics
Metadata Files
readme.md
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.
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. 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
Owner
- Name: BIMSB bioinformatics platform
- Login: BIMSBbioinfo
- Kind: organization
- Location: Berlin, Germany
- Website: bioinformatics.mdc-berlin.de
- Repositories: 83
- Profile: https://github.com/BIMSBbioinfo
git repositories for the platform
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| jona | y****e@g****m | 163 |
| Altuna Akalin | a****n@g****m | 18 |
| Oliver Nagel | o****l@f****e | 7 |
| Nitesh Turaga | n****a@g****m | 6 |
| vobencha | v****a@g****m | 4 |
| Nagel | o****l@s****t | 3 |
| LiNk-NY | m****9@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| Hervé Pagès | h****s@f****g | 1 |
| nagoli | n****i@t****e | 1 |
| Oliver Nagel | o****l@b****x | 1 |
| Jona | j****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 12
- Total pull requests: 5
- Average time to close issues: 28 days
- Average time to close pull requests: 17 days
- Total issue authors: 8
- Total pull request authors: 2
- Average comments per issue: 2.33
- Average comments per pull request: 0.6
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- al2na (4)
- jonathanronen (2)
- nikouseven (1)
- kobeho24 (1)
- ztss (1)
- sqjin (1)
- anksharm88 (1)
- nagoli104 (1)
Pull Request Authors
- nagoli104 (3)
- al2na (2)
Top Labels
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Packages
- Total packages: 3
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Total downloads:
- bioconductor 13,581 total
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Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 7
- Total maintainers: 1
proxy.golang.org: github.com/bimsbbioinfo/netsmooth
- Documentation: https://pkg.go.dev/github.com/bimsbbioinfo/netsmooth#section-documentation
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Latest release: v0.1.0
published about 8 years ago
Rankings
proxy.golang.org: github.com/BIMSBbioinfo/netSmooth
- Documentation: https://pkg.go.dev/github.com/BIMSBbioinfo/netSmooth#section-documentation
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Latest release: v0.1.0
published about 8 years ago
Rankings
bioconductor.org: netSmooth
Network smoothing for scRNAseq
- Homepage: https://github.com/BIMSBbioinfo/netSmooth
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/netSmooth/inst/doc/netSmooth.pdf
- License: GPL-3
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Latest release: 1.28.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.5 depends
- clusterExperiment >= 2.1.6 depends
- scater >= 1.15.11 depends
- DelayedArray * imports
- HDF5Array * imports
- Matrix * imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- cluster * imports
- data.table * imports
- entropy * imports
- methods * imports
- stats * imports
- BiocParallel * suggests
- BiocStyle * suggests
- NMI * suggests
- Rtsne * suggests
- STRINGdb * suggests
- biomaRt * suggests
- ggplot2 * suggests
- igraph * suggests
- knitr * suggests
- pheatmap * suggests
- rmarkdown * suggests
- testthat * suggests
- uwot * suggests