twoddpcr

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see twoddpcr.

Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

Bioconductor version: 3.16

The twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad's QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes 'definetherain' (Jones et al., 2014) and 'ddpcRquant' (Trypsteen et al., 2015) which both handle one channel ddPCR experiments only. The 'ddpcr' package available on CRAN (Attali et al., 2016) supports automatic gating of a specific class of two channel ddPCR experiments only.

Author: Anthony Chiu [aut, cre]

Maintainer: Anthony Chiu <anthony at achiu.me>

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

Installation

To install this package, start R (version "4.2") and enter:


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

BiocManager::install("twoddpcr")

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("twoddpcr")

twoddpcr: A package for Droplet Digital PCR analysis	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Software, ddPCR
Version	1.22.0
In Bioconductor since	BioC 3.5 (R-3.4) (7 years)
License	GPL-3
Depends	R (>= 3.4)
Imports	class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors
System Requirements
URL	http://github.com/CRUKMI-ComputationalBiology/twoddpcr/
Bug Reports	http://github.com/CRUKMI-ComputationalBiology/twoddpcr/issues/

Suggests	devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report

Package Archives

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

Source Package	twoddpcr_1.22.0.tar.gz
Windows Binary	twoddpcr_1.22.0.zip (64-bit only)
macOS Binary (x86_64)	twoddpcr_1.22.0.tgz
macOS Binary (arm64)	twoddpcr_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/twoddpcr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/twoddpcr
Bioc Package Browser	https://code.bioconductor.org/browse/twoddpcr/
Package Short Url	https://bioconductor.org/packages/twoddpcr/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive