Changes in version 1.12: BUG FIXES o Fix bug when generating report on Windows system o Using default graphic device for report generation Changes in version 1.10: BUG FIXES o The rqcQA function always returns list Changes in version 1.6: NEW FEATURES o Support to paired-end reads added USER VISIBLE CHANGES o Per file heatmap plot improved Changes in version 1.4: NEW FEATURES o Custom template support added o Read frequency result and plot (rqcReadFrequencyPlot) added o Per file top represented reads added o Top representated reads added o Per file heatmap plot (rqcFileHeatmap) added o checkpoint function added (experimental) USER VISIBLE CHANGES o BPPARAM argument replaced by workers argument o File information table added to default report template o Function rqcReadWidthPlot, y-axis changed to proportion (%) o Almost all plots use colorblid scheme Changes in version 1.2: NEW FEATURES o Study design metadata system (group ID, strand, etc) added o Statistics for trimming step added o Per sample mean quality box plot added o Per cycle mean quality Principal Component Analysis (PCA) plot added o Overrepresented sequencing reads plot added USER VISIBLE CHANGES o RqcResultSet class stores data as frequency tables o BPPARAM argument added to rqc and rqcQA functions BUG FIXES o Memory usage improved o Input file validation system o Rqc does not depend on X11 to generate plots o Rqc's reporter can generate plots for more than 10 files o Fixed bug related with reshape2 dependency o Fixed bug related with table function