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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

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

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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/PeacoQC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PeacoQC
Package Short Url	https://bioconductor.org/packages/PeacoQC/
Package Downloads Report	Download Stats