NEWS

CHANGES IN VERSION 1.20.1
-----------------------------
    o Add Manhattenplot functionallity
    o Bugfix in restricting for FDR correction and others (#54 and aa6e56a)
    o Ensure correct injections of outliers (#37)

CHANGES IN VERSION 1.16.1
-----------------------------
    o Add option to restrict FDR correction to sets of genes of interest
    o Add opttion to retrieve results based on those FDR values on subsets of 
      genes
    
CHANGES IN VERSION 1.7.1
-----------------------------
    o Move to S3/S4 methods to be compatible with FRASER
    o Due to the S3/S4 changes minor changes in the argument names happend 
      mainly ods -> object or x
    o Bugfixes: #29

CHANGES IN VERSION 1.3.5
-----------------------------
    o Change plotAberrantPerSample from base-R to ggplot2
    o Add plotSizeFactors
    o Minor aesthetic changes in plotting
    o Update documentation
    
CHANGES IN VERSION 1.3.2
-----------------------------
    o Documentation
    o New plot functionality
        - plotExpectedVsObservedCounts()
        - plotCountGeneSampleHeatmap()
        - plotExpressedGenes()
    o Minor bug fixes
    o Linking to publication
    
REVISED VERSION 0.99.29
-----------------------------
    o Major changes
    o Improved autoencoder model.
    o Updated API
    o Improved default parameters.

SECOND BIOCONDUCTOR SUBMISSION 0.99.10
-----------------------------
    o Smaller and faster example data set
    o Loss and gradient of loss in C++
    o Bugfixes

INITIAL BIOCONDUCTOR SUBMISSION 0.99.8
-----------------------------
    o Better documentation
    o Little changes in default values
    o Code cleanup and improvements
    o Bugfixes


R IMPLEMENTATION OF THE AUTOENCODER 0.99.7
-----------------------------
    o Adding the R implementation of the autoencoder
    o Little changes in default values
    o Updating and completing documentation
    o Bugfixes


MINOR BUGFIXES AND UPDATE OF AUTOCORRECTION 0.99.6
-----------------------------
    o Minor changes in plotting functions
    o Update interface to autoCorrection
    o Bugfixes


GITHUB RELEASE OF OUTRIDER 0.99.5
-----------------------------
    o Pre-release of OUTRIDER on GitHub


INITIAL SETUP OF OUTRIDER VERSION 0.99.2
-----------------------------
	o Initial setup of OUTRIDER package
	o Added autoCorrect (Auto Encoder) as normalization function