Changes in version 1.3.49: o plotRLE() function to make relative log expression plots to assess and compare normalizations o Refactored newSCESet() with defined hierarchy of data types o read10XResults() to read in results from 10x Chromium CellRanger output o Refined QC metrics o Bug fixes, efficiency improvements and more tests Changes in version 1.1.26: o Key code ported to C++ for greater computational and memory efficiency o Added support/integration for SC3 package for single-cell clustering o writeSCESet() function added to write SCESets to HDF5 format on disk o mergeSCESet() function to merge two SCESet objects that share features o plotPlatePosition() function to visualise gene expression and cell metadata for cells in their position on a plate o Adding plotExprsVsTxLength() to plot expression against transcript length o Added fitted line and some tweaks to plotExprsFreqVsMean(). o Adding support for scaled TPM counts when summarising expression at feature level. o Adding NULL method for set_exprs(). Adding tests. o Adding import of effective feature lengths with readKallistoResults() o runSalmon() function for running Salmon from within R, following suggestions from Rob Patro. o Added cellNames<- assignment function o Added extra QC metrics o Numerous other bug fixes and minor improvements Changes in version 0.99.3 (2016-02-29): o Package added to Bioconductor o Bioc-submission branch merged with master Changes in version 0.99.2 (2016-02-21): o Package prepared for Bioconductor submission.