twoddpcr

DOI: 10.18129/B9.bioc.twoddpcr    

This package is for version 3.9 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: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Classification, Software, ddPCR
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
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
Links To Me
Build Report

Package Archives

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

Source Package	twoddpcr_1.8.0.tar.gz
Windows Binary	twoddpcr_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	twoddpcr_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/twoddpcr
Source Repository (Developer Access)	git clone [email protected]:packages/twoddpcr
Package Short Url	https://bioconductor.org/packages/twoddpcr/
Package Downloads Report	Download Stats