Changes in version 1.28.1 o Adapt to new testthat behaviour (#87) Changes in version 1.26.2 o Add Optimal Hard Thresholding to determine optimal encoding dimension #69 o Add singular value plot for optimal encoding dimension o Add highlight.label.size to method-plot.R Changes in version 1.22.0 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