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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
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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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Software, ddPCR |
| Version | 1.0.6 |
| In Bioconductor since | BioC 3.5 (R-3.4) (0.5 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | twoddpcr_1.0.6.tar.gz |
| Windows Binary | twoddpcr_1.0.6.zip |
| Mac OS X 10.11 (El Capitan) | twoddpcr_1.0.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/twoddpcr |
| Package Short Url | http://bioconductor.org/packages/twoddpcr/ |
| Package Downloads Report | Download Stats |
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