CHANGES IN VERSION 1.4.0 ----------------------- NEW FEATURES o new arguments mapqMin and mapqMaxm in qCount, qProfile, qMeth and qExportWig allow to select alignments based on mapping quality o qAlign gains checkOnly argument which allows checking for existing alignments without triggering new alignments in case of missing ones CHANGES IN VERSION 1.2.0 ----------------------- NEW FEATURES o new miRNA-seq sample data; vignette has now workflows for ChIP-seq, RNA-seq, smRNA-seq/miRNA-seq, Bis-seq and allele-specific analysis o qMeth can report methylation states for individual molecules (reportLevel="alignment") o qCount/qProfile gain argument to ignore spliced reads in counting CHANGES IN VERSION 1.0.0 ----------------------- INITIAL RELEASE o ChIP-seq with support for single-end, paired-end and allele specific samples o RNA-seq with support for spliced alignment, single-end, paired-end and allele specific samples o Bis-seq with support for single-end, paired-end and allele specific samples