Changes in version 1.14.0 o Added the unsplitAltExps() function to reverse the effect of splitting alternative experiments. o Added a mainExpName() getter and setter to remember the name of the main experiment. o splitAltExps() will now store the chosen ref as the mainExpName. o swapAltExp() now discards the promoted experiment from the list of alternative experiments in the output. It will also exchange the colData between the swapped experiments when withColData=TRUE. These changes assist in achieving reversibility of the output. o Added applySCE() to conveniently apply a function to the main and alternative Experiments. o Added withDimnames= to reducedDim<-() and reducedDims<-(). If TRUE, these methods now emit warnings on observing incompatible row names in value. o Respect any metadata passed in with value in reducedDims<-() and altExps<-(). o Added the reduced.dim.matrix class to preserve attributes inside the reducedDims during subsetting/combining. o Setting withColData=TRUE in altExp() and altExps() will now prepend colData(x) to the output colData. o Added withDimnames= to altExp<-() and altExps<-(). If TRUE, these methods now emit warnings on observing incompatible column names in value. Also added withColData=, which will now reverse the prepending in the getter if the left-most columns are the same as colData(x). (If not the same, a warning is emitted.) Changes in version 1.12.0 o Added the rowSubset() function as a standard location for a row subset. o Added colPairs() and rowPairs() to store pairwise information (e.g., for graphs). o Added method specifications for S4Vectors compatibility. Changes in version 1.10.0 o Removed deprecated modes for getting and setting reducedDims. o Added the colLabels function as a standard location for column labels. o Added more options to control sizeFactors behavior when size factors are missing. Changes in version 1.8.0 o Added altExp() and related methods to get and set alternative Experiments. o Added the splitAltExps() utility to create many alternative Experiments at once. o Added the swapAltExp() utility to swap between main and alternative Experiments. o Deprecated isSpike(), spikeNames() and related arguments for handling spike-ins, in favor of representing spike-ins as alternative Experiments. o Deprecated type= in sizeFactors() and sizeFactorNames(), which were previously only required to store size factors for spike-ins. o Internal change to the representation of reducedDims() to streamline subsetting and combining. Changes in version 1.4.0 o Allow ... arguments to be passed to rowData() and colData(). o Added weights() methods for getting/setting observational weights. o Added reducedDimNames<- method to set the names of reduced dimension slots. o Added withDimnames= argument to reducedDim() and reducedDims(). o Exported getters and setters for internal metadata fields. o Added developer instructions for making use of internal metadata fields. Changes in version 1.2.0 o Added the clearSpikes() function to remove all spike-in information. o Added the clearSizeFactors() function to remove all size factor information. o Added the sizeFactorNames() function to query the available (named) size factor sets. o isSpike() with an unknown spike-in set in type= will no longer throw an error, and will quietly return NULL. o isSpike<- with type=NULL is deprecated in favour of clearSpikes() for removing existing spike-in information. All spike-in sets must also be explicitly named during assignment. o Added the LinearEmbeddingMatrix class for storing dimensionality reduction with loadings. Changes in version 1.0.0 o New package SingleCellExperiment, for representation of single-cell genomics data.