NEWS

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SC3 1.5.5 (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 (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 (2016-09-14)

• Added integration with 'scater' package
• Added full non-interactive support

SC3 1.1.6 (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 (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 (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 (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 (2015-12-10)

• The first version 0.99.0 is submitted to Bioconductor