ddPCRclust

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ddPCRclust.

Clustering algorithm for ddPCR data

Bioconductor version: 3.7

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 "3.5") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Clustering, Software, ddPCR

Version 1.0.1

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_1.0.1.tar.gz

Windows Binary ddPCRclust_1.0.1.zip

Mac OS X 10.11 (El Capitan) ddPCRclust_1.0.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/ddPCRclust

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ddPCRclust

Package Short Url https://bioconductor.org/packages/ddPCRclust/

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Old Source Packages for BioC 3.7 Source Archive