twoddpcr
This package is for version 3.11 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: 3.11
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("twoddpcr")):
Installation
To install this package, start R (version "4.0") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Software, ddPCR |
| Version | 1.12.0 |
| 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/ |
See More
| Suggests | devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | twoddpcr_1.12.0.tar.gz |
| Windows Binary | twoddpcr_1.12.0.zip |
| macOS 10.13 (High Sierra) | twoddpcr_1.12.0.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 3.11 | Source Archive |