Added two new options --gtf-file and --genome-version to provide additional information loaded into the cummeRbund SQLite database and its corresponding CuffSet object.
Changed options --comparison to --comparison-name and --genome_directory to --genome-directory.
Further optimised code around option parsing and removed short options where they would be confusing.
Optimised code around file path assembly, by no longer specifying the default value of the file.path fsep option.
Use paste0 instead of paste with an empty separator.
Changed the identification of replicates based on the replicate field in the replicates data frame.
Introduced conditional generation of plots, data frames and symbolic links based on file existence.
Added support for the generation of pairwise plots and data frames to break the large time dries data sets into more manageable chunks.
Added dendrogram and matrix plots indicating the number of significantly changed genes and isoforms in sample pairs.