Science Score: 26.0%
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
Found 3 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.0%) to scientific vocabulary
Repository
Flow cytometry pipeline infrastructure
Basic Info
- Host: GitHub
- Owner: UCLouvain-CBIO
- License: other
- Language: R
- Default Branch: main
- Homepage: https://uclouvain-cbio.github.io/CytoPipeline
- Size: 180 MB
Statistics
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 2
- Releases: 0
Metadata Files
README.md
Automation and visualization of flow cytometry data analysis pipelines
What is CytoPipeline?
CytoPipeline is a package that provides support for automation and
visualization of flow cytometry data analysis pipelines. In the current
state, the package focuses on the preprocessing and quality control part.
The framework is based on two main S4 classes, i.e. CytoPipeline and
CytoProcessingStep. The CytoProcessingStep defines the link between
pipeline step names and corresponding R functions that are either provided in
the CytoPipeline package itself, or exported from a third party package,
or coded by the user her/himself. The processing steps need to be specified
centrally and explicitly using either a json input file or through step by step
creation of a CytoPipeline object with dedicated methods.
After having run the pipeline, obtained results at all steps can be retrieved
and visualized thanks to file caching (the running facility uses a
BiocFileCache implementation). The package provides also specific
visualization tools like pipeline workflow summary display, and 1D/2D comparison
plots of obtained flowFrames at various steps of the pipeline.
License
The CytoPipeline code is provided under GPL license version 3.0 or
higher. The documentation,
including the manual pages and the vignettes, are distributed under a CC BY-SA
4.0 license.
Citation
If you use Cytopipeline in your research, please use the following citation:
Hauchamps P, Bayat B, Delandre S, Hamrouni M, Toussaint M, Temmerman S, Lin D, Gatto L (2024). “CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data.” BMC Bioinformatics, 25(1), 80. doi:10.1186/s12859-024-05691-z https://doi.org/10.1186/s12859-024-05691-z.
or run citation("CytoPipeline") to get the bibtex entry.
Owner
- Name: Computational Biology and Bioinformatics at UCLouvain
- Login: UCLouvain-CBIO
- Kind: organization
- Location: Brussels, Belgium
- Website: https://lgatto.github.io/cbio-lab/
- Repositories: 9
- Profile: https://github.com/UCLouvain-CBIO
GitHub Events
Total
- Watch event: 2
- Push event: 5
Last Year
- Watch event: 2
- Push event: 5
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| phauchamps | p****s@h****m | 133 |
| Philippe Hauchamps | 5****s | 14 |
| J Wokaty | j****y | 2 |
| Laurent Gatto | l****o@u****e | 2 |
Committer Domains (Top 20 + Academic)
Dependencies
- R >= 4.2 depends
- flowCore * depends
- BiocFileCache * imports
- PeacoQC * imports
- diagram * imports
- flowAI * imports
- flowClean * imports
- flowClust * imports
- flowCut * imports
- flowStats * imports
- ggcyto * imports
- ggplot2 * imports
- jsonlite * imports
- methods * imports
- openCyto * imports
- scales * imports
- stats * imports
- utils * imports
- withr * imports
- BiocStyle * suggests
- diffviewer * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
- vdiffr * suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite