hbc/bcbioRNASeq: bcbioRNASeq 0.2.4

F1000v2 manuscript release version. Major changes aggregateReplicates() support has been added back. This function returns a RangedSummarizedExperiment instead of a bcbioRNASeq object, containing only an aggregate raw counts matrix in the counts slot of assays(). The functional analysis [R Markdown][] template has been reworked to use dds_file and organism as new parameter arguments. We've reduced the number of parameters required here to run [clusterProfiler][]. Made alphaSummary() defunct for bcbioRNASeq object, in favor of DESeqDataSet only. This function is only useful when a proper design formula has been defined. Minor changes metrics() now contains an informative error for datasets that were analyzed using the fast-rnaseq [bcbio][] pipeline. DESeqDataSet coercion from bcbioRNASeq object doesn't attempt to run DESeq() command any more, which was unnecessary and improves speed. bcbioSingleCell() constructor now supports censorSamples parameter. This is useful for removing known poor quality samples upon loading. [ggplot2][] color and fill palettes are now set NULL in the quality control functions. This behavior doesn't change the appearance of the plot colors, which will still default to ggplot2::scale_colour_hue() or ggplot2::scale_fill_hue(). The upcoming [ggplot2][] v2.3.0 update supports global options for color and fill palettes, so these parameters may be deprecated in a future release. Reworked the internal code for topTables(). Infrastructure changes Added [macOS][] testing to [Travis CI][] build checks. Fixed [clusterProfiler][] compilation error on [Travis CI][] by installing libudunits2-dev (Linux)