hbc/bcbioRNASeq: bcbioRNASeq 0.2.4

F1000v2 manuscript release version.

• 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.

• 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().

• Added [macOS][] testing to [Travis CI][] build checks.
• Fixed [clusterProfiler][] compilation error on [Travis CI][] by installing libudunits2-dev (Linux).