Package: twoddpcr
Title: Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the
        number of starting molecules
Version: 1.34.0
Authors@R: person("Anthony", "Chiu",
    email="anthony@achiu.me",
    role=c("aut", "cre"))
Author: Anthony Chiu [aut, cre]
Maintainer: Anthony Chiu <anthony@achiu.me>
URL: http://github.com/CRUKMI-ComputationalBiology/twoddpcr/
BugReports: http://github.com/CRUKMI-ComputationalBiology/twoddpcr/issues/
Description: The twoddpcr package takes Droplet Digital PCR (ddPCR)
        droplet amplitude data from Bio-Rad's QuantaSoft and can
        classify the droplets. A summary of the positive/negative
        droplet counts can be generated, which can then be used to
        estimate the number of molecules using the Poisson
        distribution. This is the first open source package that
        facilitates the automatic classification of general two channel
        ddPCR data. Previous work includes 'definetherain' (Jones et
        al., 2014) and 'ddpcRquant' (Trypsteen et al., 2015) which both
        handle one channel ddPCR experiments only. The 'ddpcr' package
        available on CRAN (Attali et al., 2016) supports automatic
        gating of a specific class of two channel ddPCR experiments
        only.
Depends: R (>= 3.4)
Imports: class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
        RColorBrewer, S4Vectors
License: GPL-3
LazyData: true
RoxygenNote: 7.1.1
Collate: 'KRAScounts.R' 'KRASdata.R' 'global.R' 'ddpcrWell.R'
        'ddpcrPlate.R' 'clusterCentres.R' 'clusterStats.R' 'themes.R'
        'dropletPlot.R' 'exportTable.R' 'facetPlot.R' 'flatPlot.R'
        'ggplot.R' 'gridClassify.R' 'heatPlot.R' 'isTwoDimDataFrame.R'
        'kmeansClassify.R' 'knnClassify.R' 'mahRain.R' 'normalise.R'
        'numDroplets.R' 'parseCounts.R' 'plateSummary.R'
        'readCSVDataFrame.R' 'relabelClasses.R'
        'removeDropletClasses.R' 'sdRain.R' 'shinyVisApp.R'
        'shinyVisGlobal.R' 'shinyVisServer.R' 'shinyVisUI.R'
        'summaries.R' 'twoddpcr.R' 'wellNameSort.R'
Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
VignetteBuilder: knitr
biocViews: ddPCR, Software, Classification
Config/pak/sysreqs: make zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:37:06 UTC
RemoteUrl: https://github.com/bioc/twoddpcr
RemoteRef: RELEASE_3_22
RemoteSha: 75a6d442813d70eddab6555f79c0da2d86d476c5
NeedsCompilation: no
Packaged: 2025-11-17 07:40:02 UTC; root
Built: R 4.5.2; ; 2025-11-17 07:41:38 UTC; windows
