NEWS

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