To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

twoddpcr

 

   

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

Bioconductor version: Release (3.5)

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>

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

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 1.0.3
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
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.

Package Source twoddpcr_1.0.3.tar.gz
Windows Binary twoddpcr_1.0.3.zip
Mac OS X 10.11 (El Capitan) twoddpcr_1.0.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/twoddpcr/tree/release-3.5
Package Short Url http://bioconductor.org/packages/twoddpcr/
Package Downloads Report Download Stats

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