twoddpcr

DOI: 10.18129/B9.bioc.twoddpcr    

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

Bioconductor version: Release (3.6)

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.chiu at cruk.manchester.ac.uk>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("twoddpcr")

Documentation

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

Details

biocViews	Classification, Software, ddPCR
Version	1.2.1
In Bioconductor since	BioC 3.5 (R-3.4) (1 year)
License	GPL-3
Depends	R (>= 3.4)
Imports	class, ggplot2, hexbin, methods, scales, shiny, stats, utils, RColorBrewer, S4Vectors
LinkingTo
Suggests	devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL	http://github.com/CRUKMI-ComputationalBiology/twoddpcr/
BugReports	http://github.com/CRUKMI-ComputationalBiology/twoddpcr/issues/
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	twoddpcr_1.2.1.tar.gz
Windows Binary	twoddpcr_1.2.1.zip
Mac OS X 10.11 (El Capitan)	twoddpcr_1.2.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/twoddpcr
Package Short Url	http://bioconductor.org/packages/twoddpcr/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive