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CompensAID

This is the development version of CompensAID; for the stable release version, see CompensAID.

All versions 3.24 (devel), 3.23 (release)

Automated detection tool for spillover errors


Bioconductor version: Development (3.24)

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.

Author: Rosan Olsman [aut, cre] ORCID iD ORCID: 0000-0001-5070-0476 , Sarah Bonte [aut] ORCID iD ORCID: 0000-0002-0637-4893 , Mattias Hofmans [aut] ORCID iD ORCID: 0000-0003-2061-7617 , Malicorne Buysse [aut], Katrien Van der Borght [aut] ORCID iD ORCID: 0000-0003-1635-4359 , Yvan Saeys [aut] ORCID iD ORCID: 0000-0002-0415-1506 , Vincent van der Velden [aut] ORCID iD ORCID: 0000-0001-9457-3763 , Sofie Van Gassen [aut] ORCID iD ORCID: 0000-0002-7119-5330

Maintainer: Rosan Olsman <r.olsman at erasmusmc.nl>

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 1.1.0, https://bioconductor.org/packages/CompensAID.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("CompensAID")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CompensAID")
Overview_CompensAID HTML R Script
Reference ManualPDF
NEWSText
Need some help? Ask on the Bioconductor Support site!

Details

biocViews FlowCytometry, Preprocessing, QualityControl, Software
Version1.1.0
In Bioconductor sinceBioC 3.23 (R-4.6) (< 6 months)
License GPL (>= 3)
Depends R (>= 4.1.0)
Imports checkmate, dplyr, flowCore, flowDensity, ggcyto, ggplot2 (>= 3.5.2), methods, ParallelLogger, reshape2, rlang, stats, tibble, tidyr, utils
System Requirements
URLhttps://github.com/Olsman/CompensAID
Bug Reportshttps://github.com/Olsman/CompensAID/issues
See More
Suggests knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
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Build Report Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CompensAID_1.1.0.tar.gz
Windows Binary (x86_64) CompensAID_1.1.0.zip
macOS Binary (big-sur-x86_64) CompensAID_1.1.0.tgz
macOS Binary (sonoma-arm64) CompensAID_1.1.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/CompensAID
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/CompensAID
Package Short Url https://bioconductor.org/packages/CompensAID/
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