Changes in version 1.1.10: o Transformed correlations to a metric distance in quickCluster(). o Removed normalize() in favour of scater's normalize(). o Switched isSpike()<- to accept a character vector rather than a logical vector, to enforce naming of spike-in sets. Also added warning code when the specified spike-in sets overlap. o Allowed compute*Factors() functions to directly return the size factors. o Added selectorPlot() function for interactive plotting. o Switched to a group-based weighted correlation for one-way layouts in correlatePairs() and correlateNull(), and to a correlation of residuals for more complex design matrices. o Added phase assignments to the cyclone() output. o Implemented Brennecke et al.'s method in the technicalCV2() function. o Updated convertTo() to store spike-in-specific size factors as offsets. o Moved code and subsetting into C++ to improve memory efficiency. o Switched to loess-based trend fitting as the default in trendVar(), replaced polynomial with semi-loess fitting. o Added significance statistics to output of decomposeVar(), with only the p-values replaced by NAs for spike-ins. o Updated documentation and tests. Changes in version 1.0.0: o New package scran, for low-level analyses of single-cell RNA sequencing data.