Changes in version 1.10.0: o Fixes to all violin plots to ensure scatter matches up with violin outlines. o Rectangle categorical/categorical plots collapse to mirrored bar plots when either factor contains only one level. o Removed scater_gui(), downsampleCounts(), read10xResults(), normalizeExprs(). o Simplified plotRLE() to avoid the need for internal faceting. o Added option for row subsetting in librarySizeFactors(). o Ensured calcAverage() with subset_row= behaves as if the matrix was subsetted prior to the function call. Added support for parallelization. o Ensured calculateCPM() with subset_row= behaves as if the matrix was subsetted prior to the function call. o Added support for parallelization in nexprs(). o Added readSparseCounts() for creating a sparse matrix from a dense array on file. o Added normalizeCounts() for easy division of matrix columns by the size factors. Modified to throw error upon encountering negative, NA or zero size factors. o Added preserve_zeroes= option to normalizeSCE() for preserving sparsity with non-unity pseudo-counts. o Added runUMAP() and plotUMAP() to use the UMAP dimensionality reduction method. o Added plotExplanatoryPCs() and getExplanatoryPCs() to correlate PCs with known factors. Deprecated findImportantPCs(). o Added getVarianceExplained() to get the variance in gene expression explained by known factors. o Removed runKallisto() and runSalmon(). o Switched readTxResults() to use tximport. Switched readSalmonResults() and readKallistoResults() to use readTxResults(). o Removed obsolete fields in calculateQCMetrics(). Moved processing into C++ for a single-pass algorithm. Supported parallelization across cells for QC computations. o Added sumCountsAcrossFeatures() to sum counts across multiple redundant features. Deprecated summariseExprsAcrossFeatures(). o All plotting functions can now access internal fields by using a character vector with NA as the first element. o Returned threshold values in the attributes of the output from isOutlier(). o Deprecated the ticks in plotReducedDim(). Changes in version 1.8.0: 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 1.6.0: o Complete refactoring of the package to use the SingleCellExperiment class. Changes in version 1.4.0: 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 1.2.0: 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 1.0.0: o Package added to Bioconductor o Bioc-submission branch merged with master