Changes in version 1.20.0 o runMDS can use user-supplied function for calculating the distance matrix. runMDS can optionally store the distance matrix computed. runMDS also stores the eig and GOF fields of the object returned. o Made the handling of center, scale, color and limits similar in plotDots, plotHeatmap, and plotGroupedHeatmap o Add use_fitsne argument to runTSNE allowing the use of fast interpolated t-SNE in place of Barnes-Hut t-SNE. Changes in version 1.18.0 o Migrated many utilities to the scuttle package. o Deprecated multiplot() in favor of gridExtras::grid.arrange(). o Added swap_rownames argument to plot functions, allowing selection of genes using a rowData column. o Added column_annotation_colors argument to plotHeatmap o Changed default point aesthetics for all plots. o For runColDataPCA, reverted to documented behaviour of performing outlier detection on PCA coordinates rather than on non-transformed colData. Changes in version 1.16.0 o Added coldata_merge= argument to aggregateAcrossCells() for custom column metadata aggregation. Also include averaged reduced dimension results for each group. o Added label_format= argument to plotReducedDim() for greater control over the axis labels. o Added geometric= argument to librarySizeFactors() to compute size factors with a geometric mean. o Added the runMultiUMAP() function to perform a combined UMAP on multiple feature sets. o Added the medianSizeFactors() function to perform a DESeq2-like size factor calculation. o Modified isOutlier() so that min_diff= now acts on the log2 scale when log=TRUE. Added share_medians=, share_mads= and share_missing= options for sharing information across batches. o Exposed various developer utilities for downstream packages. o Modified sumCountsAcrossCells() to always return a SummarizedExperiment object, regardless of the class of ids. Return the number of cells used for summation in the colData. o Restored capability to create a data.frame from a SCE with makePerCellDF() and makePerFeatureDF(). o Added ggcells() and ggfeatures() for convenient creation of ggplot objects from a SCE. Changes in version 1.14.0 o Removed deprecated dplyr verbs. o Removed deprecated method= option in runPCA(). Increased ncomponents= default to 50. Deprecated use_coldata= and related options in favour of runColDataPCA(). Switched BSPARAM= default to bsparam(). o Added runColDataPCA() function for running PCA on colData(). Switch outlier detection strategy to avoid mvoutlier's dependency tree. o Added the annotateBMFeatures() function to perform annotation without modifying the input. o Pass all ... options to biomaRt::useMart() in getBMFeatureAnnos(). o Added name= arguments to runPCA(), etc. to change the name of the output reducedDim. o Added the logNormCounts() function to compute log-normalized counts in an alternative experiment-aware manner. Added a normalization-by-downsampling option via DropletUtils. o Added the perCellQCMetrics() function to compute per-cell QC metrics in an alternative experiment-aware manner. o Deprecated the normalize() method, which was considered too vague to describe what the function was actually doing. o Added the perFeatureQCMetrics() function to compute per-feature QC metrics. o Deprecated the calculateQCMetrics() function, to be replaced by the streamlined addQCPerCell() and addQCPerFeature(). o Generalized all functions, where possible, to operate on SummarizedExperiment and numeric matrices. This involved converting a number of them to S4 methods to take advantage of dispatch. Affected functions include normalizeCounts(), calculateCPM(), librarySizeFactors() and so on. o Added calculateTSNE() and related methods to operate directly on an input matrix. o Renamed the use_dimred= argument to dimred=, along with similar renamings of other arguments for consistency. o Report all percentages of variances explained as actual variances in runPCA() and getVarianceExplained(). o Added aggregateAcrossCells() and aggregateAcrossFeatures() to create a summed SingleCellExperiment object. o Added the mockSCE() function to generate example objects for the documentation. o Support multiple factors for grouping cells in sumCountsAcrossCells(). o Support list of grouping vectors in sumCountsAcrossFeatures(). o Added the order_columns_by= argument to plotHeatmap() for easy plotting by a given factor. Changed defaults to more common values. o Added a plotDots() function to create a Seurat-style dot plot. o Dropped default nmads= to 3 in isOutlier(). Changes in version 1.12.0 o Removed all functions deprecated in the last release. o Added option in runTSNE() to perform an external nearest neighbors check with BiocNeighbors. Removed the deprecated rand.seed= argument. o Added text_by= and related options to plotReducedDim(), to overlay annotation labels onto the plot. o Switched to BSPARAM= from BiocSingular for controlling SVD parameters. Deprecated the approximate= argument for runPCA(). o Switched runUMAP() to use uwot::umap. Added support for supplying a pre-defined set of nearest neighbors. o Deprecated the various dplyr verbs, i.e., filter(), arrange(), mutate(), rename(). 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