twoddpcr v1.4.1 (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