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PeacoQC

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

Peak-based selection of high quality cytometry data


Bioconductor version: Development (3.19)

This is a package that includes pre-processing and quality control functions that can remove margin events, compensate and transform the data and that will use PeacoQCSignalStability for quality control. This last function will first detect peaks in each channel of the flowframe. It will remove anomalies based on the IsolationTree function and the MAD outlier detection method. This package can be used for both flow- and mass cytometry data.

Author: Annelies Emmaneel [aut, cre]

Maintainer: Annelies Emmaneel <annelies.emmaneel at hotmail.com>

Citation (from within R, enter citation("PeacoQC")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("PeacoQC")

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("PeacoQC")
PeacoQC_Vignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews FlowCytometry, PeakDetection, Preprocessing, QualityControl, Software
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL (>=3)
Depends R (>= 4.0)
Imports circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils
System Requirements
URL http://github.com/saeyslab/PeacoQC
Bug Reports http://github.com/saeyslab/PeacoQC/issues
See More
Suggests knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me CytoPipeline
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package PeacoQC_1.13.0.tar.gz
Windows Binary PeacoQC_1.13.0.zip
macOS Binary (x86_64) PeacoQC_1.13.0.tgz
macOS Binary (arm64) PeacoQC_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PeacoQC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PeacoQC
Bioc Package Browser https://code.bioconductor.org/browse/PeacoQC/
Package Short Url https://bioconductor.org/packages/PeacoQC/
Package Downloads Report Download Stats