Introduction | Gaussian Mixture Models | Input Data | Installation | Example / Usage | Optional arguments | sampleSheetFile | B | Q | refwell | nrChannels | targetChannel | controlChannel | software | resultsToFile | plots | resPath | Threshold table columns | sample_id | thr_target | thr_ctrl | pos_dr_target | pos_dr_ctrl | tot_droplets | c_target | c_ctrl | c_norm_4Plex | c_norm_sg | q | target_assay | ctrl_assay | ref_well | PoDCall functions | importAmplitudeData() | importSampleSheet() | podcallThresholds() | podcallChannelPlot() | podcallScatterplot() | podcallHistogram() | podcallMultiplot() | PoDCall shiny application | PodCall example data | Cell Line Amplitude Data | Calculated Threshold Table | Session info
Package: PoDCall 1.20.0
Hans Petter Brodal
PoDCall: Positive Droplet Calling for DNA Methylation Droplet Digital PCR
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.
Authors:
PoDCall_1.20.0.tar.gz
PoDCall_1.20.0.zip(r-4.7-any)PoDCall_1.20.0.zip(r-4.6-any)PoDCall_1.20.0.zip(r-4.5-any)
PoDCall_1.20.0.tgz(r-4.6-any)PoDCall_1.20.0.tgz(r-4.5-any)
PoDCall_1.20.0.tar.gz(r-4.7-any)PoDCall_1.20.0.tar.gz(r-4.6-any)
PoDCall_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PoDCall/json (API)
| # Install 'PoDCall' in R: |
| install.packages('PoDCall', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- thrTable - PoDCall Example Threshold Table
On BioConductor:PoDCall-1.21.0(bioc 3.24)PoDCall-1.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
classificationepigeneticsddpcrdifferentialmethylationcpgislanddnamethylation
Last updated from:ab4d6a90b5 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 192 | ||
| linux-devel-x86_64 | NOTE | 617 | ||
| source / vignettes | OK | 203 | ||
| linux-release-x86_64 | NOTE | 649 | ||
| macos-release-arm64 | NOTE | 323 | ||
| macos-oldrel-arm64 | NOTE | 269 | ||
| windows-devel | NOTE | 721 | ||
| windows-release | NOTE | 704 | ||
| windows-oldrel | NOTE | 749 | ||
| wasm-release | OK | 121 |
Exports:importAmplitudeDataimportSampleSheetpodcallChannelPlotpodcallDdpcrpodcallHistogrampodcallMultiplotpodcallScatterplotpodcallShinypodcallThresholds
Dependencies:base64encbitbit64bslibcachemclicliprcommonmarkcpp11crayoncrosstalkdata.tabledigestdiptestDTevaluatefarverfastmapfontawesomefsggplot2gluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvisobandjquerylibjsonliteknitrlabelingLaplacesDemonlaterlazyevallifecyclemagrittrmclustmemoisemimeotelpillarpkgconfigprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrlistrmarkdownS7sassscalesshinyshinyjssourcetoolstibbletidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXMLxtableyaml
PoDCall: Positive Droplet Caller for DNA Methylation ddPCR
Last update: 2024-12-19
Started: 2020-10-23
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| importAmplitudeData | importAmplitudeData |
| importSampleSheet | importSampleSheet |
| podcallChannelPlot | podcallChannelPlot |
| Positive Droplet Calling for ddPCR | podcallDdpcr |
| podcallHistogram | podcallHistogram |
| podcallMultiplot | podcallMultiplot |
| podcallScatterplot | podcallScatterplot |
| PoDCall shiny launcher | podcallShiny |
| podcallThresholds | podcallThresholds |
| PoDCall Example Threshold Table | thrTable |
