flowGraph
Accurately selects cell populations features that differentiate between flow cytometry sample classes by removing top-down dependency between features modelled on a lattice.
Science Score: 23.0%
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○CITATION.cff file
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○codemeta.json file
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✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
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○Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary
Repository
Accurately selects cell populations features that differentiate between flow cytometry sample classes by removing top-down dependency between features modelled on a lattice.
Basic Info
- Host: GitHub
- Owner: aya49
- Language: R
- Default Branch: master
- Homepage: https://aya49.github.io/2020/09/30/flowGraph/
- Size: 4.32 MB
Statistics
- Stars: 1
- Watchers: 5
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
flowGraph
flowGraph is an R package used to identify candidate biomarkers for disease diagnosis in flow cytometry data. It does so by identifying driver cell populations whose abundance changes significantly and independently given a disease.
flowGraph takes cell counts as input and outputs SpecEnr values for each cell population within a flow cytometry sample, based on their expected proportion. SpecEnr accounts for dependencies between cell populations such that we can use it to flag only cell populations whose abundance change is incurred wholly or in part because of its association with a sample class (e.g. healthy vs sick).
Citation
The theory, proof, and algorithm behind the SpecEnr statistic used in the flowGraph package can be found in the following paper. Please consider citing if you found it helpful.
bibtex:
@article{yue2022automated,
title={Automated identification of maximal differential cell populations in flow cytometry data},
author={Yue, Alice and Chauve, Cedric and Libbrecht, Maxwell W and Brinkman, Ryan R},
journal={Cytometry Part A},
volume={101},
number={2},
pages={177--184},
year={2022},
publisher={Wiley Online Library}
}
The scripts and data from the paper can be downloaded on Zenodo.
Installation
flowGraph can be installed via Bioconductor.
You can also intall the development version directly from Github using BiocManager:
{r}
if (!require("BiocManager")) install.packages('BiocManager')
BiocManager::install("aya49/flowGraph")
This package has been tested on R version 3.5+. If you have R version 3.5 - 4.0, download this package as a zip file, go to the DESCRIPTION file, change the R version requirement, and install the package locally.
Usage
See our vignette for different use cases of the package: generating features, calculating summary statistics, visualizing results, and data specific use cases.
flowGraph takes as input a (sample x cell population) raw cell count matrix. See and example of how to obtain this matrix for one file (one row) here
flowGraph gives as output a flowGraph object that contains the SpecEnr abundance statistic and optionally its q-values. The flowGraph object can then be used to calculate more statistics, plot and visualize q-values on a cell hierarchy, etc.
```{r}
load the package
library("flowGraph) ```
Owner
- Name: Alice Yue
- Login: aya49
- Kind: user
- Location: canada
- Company: metafora biosystems
- Website: https://aya49.github.io/
- Repositories: 22
- Profile: https://github.com/aya49
researcher
GitHub Events
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- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| aya43@sfu.ca | a****3@s****a | 170 |
| Nitesh Turaga | n****a@g****m | 4 |
| Alice Yue | 2****9 | 3 |
| alice ky | a****3@a****l | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: 3 months
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
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Top Authors
Issue Authors
- HenrikBengtsson (2)
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 7,408 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: flowGraph
Identifying differential cell populations in flow cytometry data accounting for marker frequency
- Homepage: https://github.com/aya49/flowGraph
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/flowGraph/inst/doc/flowGraph.pdf
- License: Artistic-2.0
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Latest release: 1.16.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1 depends
- Matrix * imports
- Rdpack * imports
- data.table >= 1.9.5 imports
- effsize * imports
- furrr * imports
- future * imports
- ggiraph * imports
- ggplot2 * imports
- ggrepel * imports
- grDevices * imports
- gridExtra * imports
- htmlwidgets * imports
- igraph * imports
- matrixStats * imports
- methods * imports
- purrr * imports
- stats * imports
- stringi * imports
- stringr * imports
- utils * imports
- visNetwork * imports
- BiocStyle * suggests
- dplyr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 2.1.0 suggests