PeacoQC
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see PeacoQC.
Peak-based selection of high quality cytometry data
Bioconductor version: 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("PeacoQC")):
Installation
To install this package, start R (version "4.4") 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")| PeacoQC_Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FlowCytometry, PeakDetection, Preprocessing, QualityControl, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | PeacoQC_1.14.0.zip |
| macOS Binary (x86_64) | PeacoQC_1.14.0.tgz |
| macOS Binary (arm64) | PeacoQC_1.14.0.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 |