Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
Bioconductor version: Release (3.12)
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.
Secure data export — QuantaSoft data table can be exported as secure PDF For optimal performance, it is recommended that users use the laptop sold by Bio-Rad for the QX100 or QX200 ddPCR System. Download the instruction manual to learn more about QuantaSoft Software, Regulatory Edition and the QX200 Droplet Digital PCR System. DdpcRquant is made for 1-D analysis (Bio-Rad qx100/qx200). 1 channel at a time. If 2 channels per well = one after the other will be analyzed Use the NTCs to calculate a single threshold. Whether the extreme value measured in the NTC is a real or false positive value is beyond the scope of ddpcrquant ddpcRquant uses a predefined.
- Highly accurate and sensitive diagnostic detection of SARS-COV-2 by digital PCR. Medrxiv (Mar 2020).
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Author: Anthony Chiu [aut, cre]
Maintainer: Anthony Chiu <anthony at achiu.me>
Citation (from within R, enter citation('twoddpcr')):
Quantasoft Analysis Pro Software
Installation
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Documentation
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| HTML | R Script | twoddpcr: A package for Droplet Digital PCR analysis |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Software, ddPCR |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (4 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.
Bio Rad Quantasoft Mac Download
| Source Package | twoddpcr_1.14.0.tar.gz |
| Windows Binary | twoddpcr_1.14.0.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | twoddpcr_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/twoddpcr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/twoddpcr |
| Package Short Url | https://bioconductor.org/packages/twoddpcr/ |
| Package Downloads Report | Download Stats |