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PoDCall

This is the development version of PoDCall; for the stable release version, see PoDCall.

Positive Droplet Calling for DNA Methylation Droplet Digital PCR


Bioconductor version: Development (3.19)

Reads files exported from 'QX Manager or 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>

Citation (from within R, enter citation("PoDCall")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Classification, CpGIsland, DNAMethylation, DifferentialMethylation, Epigenetics, Software, ddPCR
Version 1.11.2
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.4)
Imports ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils
System Requirements
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Suggests knitr, rmarkdown, testthat, BiocStyle
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Package Archives

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

Source Package PoDCall_1.11.2.tar.gz
Windows Binary PoDCall_1.11.2.zip (64-bit only)
macOS Binary (x86_64) PoDCall_1.11.2.tgz
macOS Binary (arm64) PoDCall_1.11.2.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