Changes in version 1.7.18:

    o   Refactored calculateQCMetrics() to ignore potential non-linearity,
	 rank genes by highest expression, rename automatically generated
	 union sets, allow for output of a compact format.

    o   Refactored all plotting functions to allow access to nested fields
	 in the colData() or rowData(), by supplying a character vector.

    o   Refactored plotTSNE(), plotPCA(), etc. to dispatch to the
	 calculation functions (e.g., runTSNE(), runPCA()), with argument
	 checks.

    o   Refactored plotColData() and plotRowData() to use the same argument
	 types as other functions rather than aes= input.

    o   Removed all plotting functions that do not operate on
	 SingleCellExperiment objects.

    o   Deprecated read10xResults(), downsampleCounts() in favour of methods
	 from the DropletUtils package.

    o   Deprecated scater_gui() in favour of methods from the iSEE package.

    o   Deprecated normalizeExprs() as this function made very little sense.

    o   Added plotHeatmap() function, for easy plotting of heatmaps.

    o   Added librarySizeFactors() function, to compute size factors from
	 library sizes.

    o   Added by_exprs_values= argument to many plotting functions, to
	 distinguish direct plotting of expression values from their use in
	 aesthetics.

    o   Renamed arguments in plotHighestExprs(), plotExprsVsTxLength(),
	 plotExprsFreqVsMean() for greater clarity.

    o   Added centreSizeFactors() function for centralized size factor
	 centering.

    o   Added size_factor_grouping= argument to normalizeSCE(),
	 calcAverage() and calculateCPM().

    o   Added subset_row= argument to calculateCPM().

    o   Consolidated size_factors= argument into use_size_factors= for
	 calcAverage(), calculateCPM().

    o   Modified normalizeSCE() so that centre_size_factors=FALSE does not
	 use centred size factors at all during normalization.

Changes in version 1.5.11:

    o   Complete refactoring of the package to use the SingleCellExperiment
	 class

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.