diffcyt
R package for differential discovery analyses in high-dimensional cytometry data
Science Score: 33.0%
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
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: nature.com -
✓Committers with academic emails
1 of 10 committers (10.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary
Keywords from Contributors
Repository
R package for differential discovery analyses in high-dimensional cytometry data
Basic Info
Statistics
- Stars: 21
- Watchers: 6
- Forks: 12
- Open Issues: 34
- Releases: 0
Metadata Files
README.md
diffcyt
Introduction
diffcyt: R package for differential discovery in high-dimensional cytometry via high-resolution clustering
The diffcyt package implements statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.
Details and citation
For details on the statistical methodology and comparisons with existing approaches, see our paper:
Tutorial and examples
For a tutorial and examples of usage, see the Bioconductor package vignette (link also available via the main Bioconductor page for the diffcyt package).
Installation
The diffcyt package is available from Bioconductor, and can be installed as follows:
```{r}
Install Bioconductor installer from CRAN
install.packages("BiocManager")
Install 'diffcyt' package from Bioconductor
BiocManager::install("diffcyt") ```
To run the examples in the package vignette and generate additional visualizations, the HDCytoData and CATALYST packages from Bioconductor are also required.
{r}
BiocManager::install(c("HDCytoData", "CATALYST"))
Owner
- Name: Lukas Weber
- Login: lmweber
- Kind: user
- Location: Boston, MA
- Company: Boston University
- Website: https://lmweber.org/
- Repositories: 75
- Profile: https://github.com/lmweber
Assistant Professor, Department of Biostatistics, Boston University
GitHub Events
Total
- Issues event: 5
- Watch event: 1
- Issue comment event: 14
- Push event: 8
- Pull request event: 2
- Create event: 3
Last Year
- Issues event: 5
- Watch event: 1
- Issue comment event: 14
- Push event: 8
- Pull request event: 2
- Create event: 3
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lukas Weber | l****r@g****m | 360 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| fionarhuang | f****g@g****m | 3 |
| vobencha | v****a@g****m | 2 |
| Mark Robinson | m****n@m****h | 2 |
| vobencha | v****n@r****g | 2 |
| Kayla-Morrell | k****l@r****g | 1 |
| Hervé Pagès | h****s@f****g | 1 |
| markrobinsonuzh | m****n@i****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 57
- Total pull requests: 7
- Average time to close issues: 20 days
- Average time to close pull requests: 25 days
- Total issue authors: 44
- Total pull request authors: 5
- Average comments per issue: 2.21
- Average comments per pull request: 0.71
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 2
- Average time to close issues: 2 days
- Average time to close pull requests: 5 days
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 0.5
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- LukaTandaric (3)
- jenkinmt (3)
- algebio (2)
- cr2106 (2)
- tammyyyx (2)
- paulyashna (2)
- lmweber (2)
- ramay (2)
- shanh1 (2)
- SamGG (2)
- denvercal1234GitHub (2)
- Almr95 (1)
- Stein-ErikG (1)
- antoine4ucsd (1)
- MayaCyTOFnewbie (1)
Pull Request Authors
- markrobinsonuzh (3)
- HelenaLC (1)
- igordot (1)
- retogerber (1)
- fionarhuang (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 40,077 total
- Total dependent packages: 5
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: diffcyt
Differential discovery in high-dimensional cytometry via high-resolution clustering
- Homepage: https://github.com/lmweber/diffcyt
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/diffcyt/inst/doc/diffcyt.pdf
- License: MIT + file LICENSE
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Latest release: 1.28.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.4.0 depends
- ComplexHeatmap * imports
- FlowSOM * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- circlize * imports
- dplyr * imports
- edgeR * imports
- flowCore * imports
- grDevices * imports
- graphics * imports
- grid * imports
- limma * imports
- lme4 * imports
- magrittr * imports
- methods * imports
- multcomp * imports
- reshape2 * imports
- stats * imports
- tidyr * imports
- utils * imports
- BiocStyle * suggests
- CATALYST * suggests
- HDCytoData * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests