PoDCall
Positive Droplet Calling for DNA Methylation Droplet Digital PCR
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PoDCall")Details
| Maintainer | Hans Petter Brodal <h.p.brodal@ous-research.no> |
| Author | Hans Petter Brodal [aut, cre], Marine Jeanmougin [aut], Guro Elisabeth Lind [aut] |
| License | GPL-3 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, CpGIsland, DNAMethylation, DifferentialMethylation, Epigenetics, Software, ddPCR |
| Package Short Url | https://bioconductor.org/packages/PoDCall/ |
Citation
From within R, enter citation("PoDCall"):
Hans Petter Brodal, Marine Jeanmougin, Guro Elisabeth Lind. PoDCall: Positive Droplet Calling for DNA Methylation Droplet Digital PCR. doi:10.18129/B9.bioc.PoDCall, R package version 1.20.0, https://bioconductor.org/packages/PoDCall.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PoDCall_1.20.0.tar.gz |
| Windows binary (x86_64) | PoDCall_1.20.0.zip |
| macOS binary (arm64) | PoDCall_1.20.0.tgz |
| macOS binary (x86_64) | PoDCall_1.20.0.tgz |