PeacoQC

DOI: 10.18129/B9.bioc.PeacoQC  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see PeacoQC.

Peak-based selection of high quality cytometry data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

PDF	R Script	PeacoQC_Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	FlowCytometry, PeakDetection, Preprocessing, QualityControl, Software
Version	1.10.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	GPL (>=3)
Depends	R (>= 4.0)
Imports	circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2, grDevices, grid, gridExtra, methods, plyr, stats, utils
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	http://github.com/saeyslab/PeacoQC
BugReports	http://github.com/saeyslab/PeacoQC/issues
Depends On Me
Imports Me	CytoPipeline
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	PeacoQC_1.10.0.tar.gz
Windows Binary	PeacoQC_1.10.0.zip
macOS Binary (x86_64)	PeacoQC_1.10.0.tgz
macOS Binary (arm64)	PeacoQC_1.10.0.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