SC3 News SC3 1.5.5 (Release date: 2017-10-19): * `scater` now works based on `SingleCellExperiment` class * `sc3` slot has moved to the `metadata` slot of `SingleCellExperiment` class * `scater` class is completely deprecated from `SC3` * All `scater` functionality can work on `SingleCellExperiment` class * Clustering logic hasn't been changed at all SC3 1.3.7 (Release date: 2016-11-23): * RSelenium functionality is removed due to no further support * All results (clustering and biology) are now written to phenoData and featureData slots of the input 'SCESet' object * 'Labels' and 'Cell Outliers' tabs in the interactive shiny session are removed, because these data can now be visualized on the other heatmaps SC3 1.1.7 (Release date: 2016-09-14): * Added integration with `scater` package * Added full non-interactive support SC3 1.1.6 (Release date: 2016-08-04): * Optimised distance and consensus calculations using Rccp * Optimised some other bits and pieces * `SC3` is now up to 2 times faster for 1000 cells datasets SC3 1.1.5 (Release date: 2016-06-28): * Added svm.train.inds parameter - it allows a user to train SVM on a selected subset of cells SC3 0.99.37 (Release date: 2016-04-15): * tSNE panel is added to the interactive session * additional table has been added to the output - it contains original and new cell labels in the order corresponding to the order of cells in the input expression matrix * three functions corresponding to biological interpretation are now exported and can be used manually: get_de_genes, get_marker_genes, get_outl_cells. See their documentation for more details * several bugs have been fixed SC3 0.99.23 (Release date: 2016-03-01): * Major redesign * Added description panels * Fixed a bug with RSelenium * Added a proper Excel export using WriteXLS library SC3 0.99.0 (Release date: 2015-12-10): * The first version 0.99.0 is submitted to Bioconductor