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ddPCRclust

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

Clustering algorithm for ddPCR data


Bioconductor version: Development (3.19)

The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.

Author: Benedikt G. Brink [aut, cre], Justin Meskas [ctb], Ryan R. Brinkman [ctb]

Maintainer: Benedikt G. Brink <bbrink at cebitec.uni-bielefeld.de>

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

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("ddPCRclust")

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("ddPCRclust")
Bioconductor LaTeX Style PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, Software, ddPCR
Version 1.23.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License Artistic-2.0
Depends R (>= 3.5)
Imports plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore, flowDensity(>= 1.13.3), SamSPECTRAL, flowPeaks
System Requirements
URL https://github.com/bgbrink/ddPCRclust
Bug Reports https://github.com/bgbrink/ddPCRclust/issues
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Package Archives

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

Source Package ddPCRclust_1.23.0.tar.gz
Windows Binary ddPCRclust_1.23.0.zip
macOS Binary (x86_64) ddPCRclust_1.23.0.tgz
macOS Binary (arm64) ddPCRclust_1.23.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ddPCRclust
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ddPCRclust
Bioc Package Browser https://code.bioconductor.org/browse/ddPCRclust/
Package Short Url https://bioconductor.org/packages/ddPCRclust/
Package Downloads Report Download Stats