twoddpcr v1.5.1 (Devel release date: 2018-05-21) ============ Update contact details of maintainer. twoddpcr v1.3.1 (Devel release date: 2018-01-10) ============ Bug fixes: * Fix Issue #2: The 'plotLimits' parameter now works as intended for the 'facetPlot' function when used with the 'cMethod' parameter. twoddpcr v1.1.3 (Devel release date: 2017-07-31) ============ New features: * Unit tests for facetPlot. twoddpcr v1.1.2 (Devel release date: 2017-07-28) ============ New features: * facetPlot now has a new 'cMethod' parameter for plotting the classifications against each other. twoddpcr v1.1.1 (Devel release date: 2017-07-17) ============ Bug fixes: * Merge all bug fixes below. twoddpcr v1.0.6 (Release date: 2017-06-08) ============ Bug fixes: * Fix Issue #1 further: Catch all errors from uploading droplet amplitude CSVs. twoddpcr v1.0.5 (Release date: 2017-06-01) ============ Bug fixes: * Fix Issue #1 further: Stop the Shiny app from crashing when one channel data or data in the wrong format is uploaded. Emphasis throughout that only two channel data is accepted. * Make all hyperlinks open in a new tab/page. This prevents the user from accidentally ending a session in the app. twoddpcr v1.0.4 (Release date: 2017-05-30) ============ Bug fixes: * Fix Issue #1: Loading a QuantaSoft classification no longer looks for a column named "Cluster". twoddpcr v1.0.3 (Release date: 2017-05-26) ============ Bug fixes: * Ensure that the Rmd template is copied for report generation in the Shiny app. twoddpcr v1.0.2 (Release date: 2017-05-05) ============ Documentation: * Update the citation information for the Bioinformatics paper. twoddpcr v1.0.1 (Release date: 2017-05-04) ============ Documentation: * In the Shiny app, add a reference to the Bioconductor vignette comparing the classification methods. Bug fixes: * Minor fix removing conflicts in the dropletPlot documentation. twoddpcr v1.0.0 (Release date: 2017-04-25) ============ First full release incorporating all of the devel updates. twoddpcr v0.99.2 (Release date: 2017-03-21) ============ Updates as suggested by anonymous reviewers. Shiny app: * Simple dynamic HTML report generation. * Re-use the user-specified labels in plots and tables (where possible). NN, NP, PN and PP are still used internally and for file input/output. * Add captions to pages, improve the help sidebars and page. Vignette: * Describe the KRASdata dataset. * Compare the classification methods with discussion. Bug fixes: * k-means failed when only one class was present. twoddpcr v0.99.1 (Release date: 2017-02-16) ============ More R-like changes as suggested by Martin Morgan at Bioconductor. Main changes: * ddpcrPlate objects can be subsetted like a list * The amplitudes() function replaces getDroplets() and getAllDroplets() * wellClassification() and plateClassification() replace the old get/set methods and can be set using <- * Changes to improve the robustness and clarity of the code twoddpcr v0.99.0 (Release date: 2017-01-24) ============ First devel release. twoddpcr is an R package for Droplet Digitial PCR (ddPCR) analysis. The name of the package reflects the package's support for analysing two channel ddPCR data. Key functionality: * Create ddpcrPlate objects * kmeansClassify() classifies droplets using k-means clustering * mahalanobisRain() refines the classification, removing ambiguous droplets