Science Score: 49.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 16 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
4 of 26 committers (15.4%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Simple simulation of single-cell RNA sequencing data
Basic Info
- Host: GitHub
- Owner: Oshlack
- License: gpl-3.0
- Language: R
- Default Branch: devel
- Homepage: http://oshlacklab.com/splatter/
- Size: 57.2 MB
Statistics
- Stars: 228
- Watchers: 5
- Forks: 59
- Open Issues: 8
- Releases: 17
Topics
Metadata Files
README.md
Splatter
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Splatter is an R package for the simple simulation of single-cell RNA sequencing data. Splatter provides a common interface to multiple simulations that have:
- Functions for estimating simulation parameters
- Objects for storing those parameters
- Functions for simulating counts using those parameters
Splatter is built on top of several Bioconductor packages and stores simulations in SingleCellExperiment objects.
Splatter also has functions for comparing simulations and real datasets.
Installation.
Splatter is available from Bioconductor for R >=3.4.
It can be installed from Bioconductor with:
r
if (!requireNamespace("BiocManager", quietly=TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("splatter")
If you wish to build a local version of the vignette use:
r
BiocManager::install("splatter", build_vignettes=TRUE)
This will also build the vignette and install all suggested dependencies (which aren't required for core functionality).
Getting started
Once installed the best place to get started is the vignette. For most users the most convenient way to access this is online here. To get started with population scale simulations, see the splatPop vignette here.
Alternatively, if you chose to build the vignette, you can load Splatter, then browse the vignettes:
r
library(splatter)
browseVignettes("splatter")
This is a detailed document that introduces the main features of Splatter.
Citing Splatter
If you use Splatter please cite our paper "Zappia L, Phipson B, Oshlack A. Splatter: Simulation Of Single-Cell RNA Sequencing Data. Genome Biology. 2017; doi:10.1186/s13059-017-1305-0".
bibtex
@Article{,
author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
title = {Splatter: simulation of single-cell RNA sequencing data},
journal = {Genome Biology},
year = {2017},
url = {http://dx.doi.org/10.1186/s13059-017-1305-0},
doi = {10.1186/s13059-017-1305-0},
}
If you use the splatPop functions, please also cite "Azodi CB, Zappia L, Oshlack A, McCarthy DJ. splatPop: simulating population scale single-cell RNA sequencing data. Genome Biology. 2021; doi:10.1186/s13059-021-02546-1".
bibtex
@Article{,
author = {Christina B Azodi and Luke Zappia and Alicia Oshlack and Davis J McCarthy},
title = {splatPop: simulating population scale single-cell RNA sequencing data},
journal = {Genome Biology},
year = {2021},
url = {http://dx.doi.org/10.1186/s13059-021-02546-1},
doi = {10.1186/s13059-021-02546-1},
}
Owner
- Name: Oshlack
- Login: Oshlack
- Kind: organization
- Repositories: 38
- Profile: https://github.com/Oshlack
GitHub Events
Total
- Create event: 10
- Release event: 2
- Issues event: 2
- Watch event: 10
- Delete event: 7
- Issue comment event: 2
- Push event: 20
- Pull request event: 12
- Fork event: 2
Last Year
- Create event: 10
- Release event: 2
- Issues event: 2
- Watch event: 10
- Delete event: 7
- Issue comment event: 2
- Push event: 20
- Pull request event: 12
- Fork event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Luke Zappia | l****i | 542 |
| cazodi | c****i@s****u | 83 |
| Nitesh Turaga | n****a@g****m | 15 |
| Luke Zappia | l****a@m****u | 13 |
| l.zappia | l****a@b****8 | 9 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 5 |
| Hervé Pagès | h****s@f****g | 4 |
| Robrecht Cannoodt | b****s@g****m | 4 |
| Christina Azodi | c****i@g****m | 4 |
| Robrecht Cannoodt | r****t@u****e | 3 |
| evanbiederstedt | e****t@g****m | 3 |
| Wenjie Wang | w****g@l****m | 3 |
| J Wokaty | j****y@s****u | 2 |
| vobencha | v****a@g****m | 2 |
| J Wokaty | j****y | 2 |
| Herve Pages | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| LiNk-NY | m****9@g****m | 2 |
| Wouter Saelens | w****s@g****m | 1 |
| Allen Zhang | a****g@b****a | 1 |
| Jeffrey Pullin | j****n@g****m | 1 |
| Dayne | d****r@g****m | 1 |
| Christina Azodi | c****i@m****u | 1 |
| lshep | l****d@r****g | 1 |
| mtmorgan@fhcrc.org | m****n@f****g@b****8 | 1 |
| Martin Morgan | m****n@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 0
- Total pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: about 7 hours
- Total issue authors: 0
- Total pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: about 7 hours
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- kuang-da (1)
- emine2441 (1)
- vali301s (1)
- HelenaLC (1)
Pull Request Authors
- dependabot[bot] (5)
- lazappi (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 4.0 depends
- SingleCellExperiment * depends
- BiocGenerics * imports
- BiocParallel * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- checkmate >= 2.0.0 imports
- crayon * imports
- edgeR * imports
- fitdistrplus * imports
- ggplot2 * imports
- grDevices * imports
- locfit * imports
- matrixStats * imports
- methods * imports
- scales * imports
- scater >= 1.15.16 imports
- stats * imports
- utils * imports
- BASiCS >= 1.7.10 suggests
- BiocManager * suggests
- BiocSingular * suggests
- BiocStyle * suggests
- Biostrings * suggests
- GenomeInfoDb * suggests
- GenomicRanges * suggests
- IRanges * suggests
- SparseDC * suggests
- VariantAnnotation * suggests
- covr * suggests
- cowplot * suggests
- igraph * suggests
- knitr * suggests
- limSolve * suggests
- lme4 * suggests
- magick * suggests
- mfa * suggests
- phenopath * suggests
- preprocessCore * suggests
- progress * suggests
- pscl * suggests
- rmarkdown * suggests
- scDD * suggests
- scran * suggests
- scuttle * suggests
- spelling * suggests
- testthat * suggests
- zinbwave * suggests
- JamesIves/github-pages-deploy-action 4.1.4 composite
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite