PoDCall

DOI: 10.18129/B9.bioc.PoDCall  

Positive Droplet Calling for DNA Methylation Droplet Digital PCR

Bioconductor version: Release (3.17)

Reads files exported from 'QuantaSoft' containing amplitude values from a run of ddPCR (96 well plate) and robustly sets thresholds to determine positive droplets for each channel of each individual well. Concentration and normalized concentration in addition to other metrics is then calculated for each well. Results are returned as a table, optionally written to file, as well as optional plots (scatterplot and histogram) for both channels per well written to file. The package includes a shiny application which provides an interactive and user-friendly interface to the full functionality of PoDCall.

Author: Hans Petter Brodal [aut, cre], Marine Jeanmougin [aut], Guro Elisabeth Lind [aut]

Maintainer: Hans Petter Brodal <hans.petter.brodal at rr-research.no>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("PoDCall")

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("PoDCall")

 

HTML	R Script	PoDCall: Positive Droplet Caller for DNA Methylation ddPCR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, CpGIsland, DNAMethylation, DifferentialMethylation, Epigenetics, Software, ddPCR
Version	1.8.0
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 years)
License	GPL-3
Depends	R (>= 4.3)
Imports	ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL
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	PoDCall_1.8.0.tar.gz
Windows Binary	PoDCall_1.8.0.zip
macOS Binary (x86_64)	PoDCall_1.8.0.tgz
macOS Binary (arm64)	PoDCall_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PoDCall
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PoDCall
Bioc Package Browser	https://code.bioconductor.org/browse/PoDCall/
Package Short Url	https://bioconductor.org/packages/PoDCall/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive