CompensAID
Automated detection tool for spillover errors
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The CompensAID is an automated quality control tool, which determines for each marker combination in the FCS file, whether there a potential presence of reference errors. Such reference errors, which represent themselves in the form of skewed populations, are detected by integrating the Secondary Stain Index (SSI) score. Marker combinations with an SSI < 1 are flagged by CompensAID.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CompensAID")Details
| Maintainer | Rosan Olsman <r.olsman@erasmusmc.nl> |
| Author | Rosan Olsman [aut, cre] (ORCID: <https://orcid.org/0000-0001-5070-0476>), Sarah Bonte [aut] (ORCID: <https://orcid.org/0000-0002-0637-4893>), Mattias Hofmans [aut] (ORCID: <https://orcid.org/0000-0003-2061-7617>), Malicorne Buysse [aut], Katrien Van der Borght [aut] (ORCID: <https://orcid.org/0000-0003-1635-4359>), Yvan Saeys [aut] (ORCID: <https://orcid.org/0000-0002-0415-1506>), Vincent van der Velden [aut] (ORCID: <https://orcid.org/0000-0001-9457-3763>), Sofie Van Gassen [aut] (ORCID: <https://orcid.org/0000-0002-7119-5330>) |
| License | GPL (>= 3) |
| URL | https://github.com/Olsman/CompensAID |
| Bug Reports | https://github.com/Olsman/CompensAID/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | FlowCytometry, Preprocessing, QualityControl, Software |
| Package Short Url | https://bioconductor.org/packages/CompensAID/ |
Citation
From within R, enter citation("CompensAID"):
Rosan Olsman, Sarah Bonte, Mattias Hofmans, Malicorne Buysse, Katrien Van der Borght, Yvan Saeys, Vincent van der Velden, Sofie Van Gassen. CompensAID: Automated detection tool for spillover errors. doi:10.18129/B9.bioc.CompensAID, R package version 1.0.0, https://bioconductor.org/packages/CompensAID.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CompensAID_1.0.0.tar.gz |
| Windows binary (x86_64) | CompensAID_1.0.0.zip |
| macOS binary (arm64) | CompensAID_1.0.0.tgz |
| macOS binary (x86_64) | CompensAID_1.0.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: checkmate, dplyr, flowCore, flowDensity, ggcyto, ggplot2 (>= 3.5.2), methods, ParallelLogger, reshape2, rlang, stats, tibble, tidyr, utils
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle