CHANGES IN VERSION 1.40.0 ------------------------- USER-VISIBLE CHANGES o count bam alignments with coordinates but flag 'unmapped' (e.g. generated by hisat2) as mapped, so that qCount, qQCReport and alignmentStats are consistent CHANGES IN VERSION 1.34.0 ------------------------- USER-VISIBLE CHANGES o removed automatic downloading and installation of BSgenome references o added option to parallelize qExportWig CHANGES IN VERSION 1.30.0 ------------------------- NEW FEATURES o added binSize argument for qProfile CHANGES IN VERSION 1.24.0 ------------------------- NEW FEATURES o added support for spliced alignments using HISAT2 (via Rhisat2 package) o migrated from Rsamtools to Rhtslib C library for operations on bam files o migrated unit test from RUnit to testthat o ignore reference deletions (BAM_CDEL) in qCount(..., reportLevel = "junction") CHANGES IN VERSION 1.10.0 ------------------------- NEW FEATURES o qExportWig gained createBigWig argument and can now create bigWig files directly o qQCReport now also produces base quality plots for bam-file projects by sampling reads from the bam files o qCount, qProfile and qExportWig have gained a includeSecondary argument to include/exclude secondary alignments while counting CHANGES IN VERSION 1.8.0 ----------------------- PUBLICATION o A paper describing the QuasR package has been published (see citation("QuasR")): Gaidatzis D. et al., Bioinformatics, 2015. doi: 10.1093/bioinformatics/btu781 NEW FEATURES o started implementing support for BiocParallel, allowing QuasR to also run on batch clusters (support is currently limited to qQCReport) 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