PoDCall
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see PoDCall.
Positive Droplet Calling for DNA Methylation Droplet Digital PCR
Bioconductor version: 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>
citation("PoDCall")):
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")| PoDCall: Positive Droplet Caller for DNA Methylation ddPCR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, CpGIsland, DNAMethylation, DifferentialMethylation, Epigenetics, Software, ddPCR |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.3) |
| Imports | ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT, LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils |
| System Requirements | |
| URL |
See More
| Suggests | knitr, 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 | 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 |