PeacoQC

DOI: 10.18129/B9.bioc.PeacoQC    

Peak-based selection of high quality cytometry data

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script PeacoQC_Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews FlowCytometry, PeakDetection, Preprocessing, QualityControl, Software
Version 0.99.25
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package PeacoQC_0.99.25.tar.gz
Windows Binary PeacoQC_0.99.25.zip (32- & 64-bit)
macOS 10.13 (High Sierra) PeacoQC_0.99.25.tgz
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

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