Science Score: 20.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
3 of 15 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.9%) to scientific vocabulary
Keywords from Contributors
Repository
Normalization for single cell RNA-seq data
Basic Info
- Host: GitHub
- Owner: rhondabacher
- Language: R
- Default Branch: devel
- Size: 41.3 MB
Statistics
- Stars: 48
- Watchers: 3
- Forks: 10
- Open Issues: 16
- Releases: 0
Metadata Files
README.md
SCnorm: robust normalization of single-cell RNA-seq data
SCnorm is an R package which can be used to normalize single-cell RNA-seq data. SCnorm is on Bioconductor and instructions for download may be found at https://bioconductor.org/packages/release/bioc/html/SCnorm.html.
Can you use SCnorm on your 10X (or very sparse) dataset?
SCnorm is not intended for datasets with more than ~80% zero counts, often K will not converge in these situations. Setting the FilterExpression parameter to 1 or 2 may help, but is not a guarantee. It may also be helpful to use the ditherCounts = TRUE parameter for sparse UMI based data which may contain numerous tied counts (counts of 1 and 2 for example).
Additional details and a FAQ for SCnorm are described in the vignette: SCnorm Vignette
Installation
Make sure to use the latest version of SCnorm by installing it from BioConductor or GitHub.
R
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("SCnorm")
or
R
library(devtools)
devtools::install_github("rhondabacher/SCnorm")
To access a version of SCnorm that does not require R version >= 3.4 you can
download SCnorm from the development branch here:
https://github.com/rhondabacher/SCnorm/tree/devel
Author
Rhonda Bacher rhonda.bacher@gmail.com
Cite
Please cite SCnorm if you use it in your research:
Bacher R, Chu LF, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton M, Kendziorski C. SCnorm: robust normalization of single-cell RNA-seq data. Nature Methods. 2017 Jun 1;14(6):584-6. https://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4263.html
Latest Update: v1.5.7
Added additional warnings when using the useSpikes option and SCnorm now supports input data in the sparse matrix format.
Previous updates: v1.5.4
Allow separate normalizations for different Conditions for very large dataset. See vignette for example.
Owner
- Name: Rhonda Bacher
- Login: rhondabacher
- Kind: user
- Location: Gainesville, FL
- Company: University of Florida
- Website: www.rhondabacher.com
- Repositories: 3
- Profile: https://github.com/rhondabacher
Assistant Professor of Biostatistics
GitHub Events
Total
- Issues event: 2
- Delete event: 1
- Issue comment event: 2
- Push event: 1
- Create event: 1
Last Year
- Issues event: 2
- Delete event: 1
- Issue comment event: 2
- Push event: 1
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Rhonda Bacher | r****r@g****m | 96 |
| Rhonda Bacher | r****r@w****u | 16 |
| Nitesh Turaga | n****a@g****m | 14 |
| Rhonda Bacher | r****r | 4 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
| vobencha | v****a@g****m | 2 |
| LiNk-NY | m****9@g****m | 2 |
| vobencha | v****n@r****g | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| Martin Morgan | m****n@f****g | 1 |
| Alain Domissy | a****y@g****m | 1 |
| Jens Preussner | j****r@m****e | 1 |
| Ryan | n****s@g****m | 1 |
| Jens Preußner | j****r | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 3
-
Total downloads:
- bioconductor 23,246 total
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 22
- Total maintainers: 1
proxy.golang.org: github.com/rhondabacher/scnorm
- Documentation: https://pkg.go.dev/github.com/rhondabacher/scnorm#section-documentation
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Latest release: v1.5.7
published over 7 years ago
Rankings
proxy.golang.org: github.com/rhondabacher/SCnorm
- Documentation: https://pkg.go.dev/github.com/rhondabacher/SCnorm#section-documentation
-
Latest release: v1.5.7
published over 7 years ago
Rankings
bioconductor.org: SCnorm
Normalization of single cell RNA-seq data
- Homepage: https://github.com/rhondabacher/SCnorm
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/SCnorm/inst/doc/SCnorm.pdf
- License: GPL (>= 2)
-
Latest release: 1.30.1
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.4.0 depends
- BiocGenerics * imports
- BiocParallel * imports
- S4Vectors * imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- cluster * imports
- data.table * imports
- forcats * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- methods * imports
- moments * imports
- parallel * imports
- quantreg * imports
- stats * imports
- BiocStyle * suggests
- devtools * suggests
- knitr * suggests
- rmarkdown * suggests