NEWS
QuasR 1.40.0
USER-VISIBLE CHANGES
- count bam alignments with coordinates but flag 'unmapped' (e.g. generated by hisat2) as mapped, so that qCount, qQCReport and alignmentStats are consistent
QuasR 1.34.0
USER-VISIBLE CHANGES
- removed automatic downloading and installation of BSgenome references
- added option to parallelize qExportWig
QuasR 1.30.0
NEW FEATURES
- added binSize argument for qProfile
QuasR 1.24.0
NEW FEATURES
- added support for spliced alignments using HISAT2 (via Rhisat2 package)
- migrated from Rsamtools to Rhtslib C library for operations on bam files
- migrated unit test from RUnit to testthat
- ignore reference deletions (BAM_CDEL) in qCount(..., reportLevel = "junction")
QuasR 1.10.0
NEW FEATURES
- qExportWig gained createBigWig argument and can now create bigWig files directly
- qQCReport now also produces base quality plots for bam-file projects by sampling reads from the bam files
- qCount, qProfile and qExportWig have gained a includeSecondary argument to include/exclude secondary alignments while counting
QuasR 1.8.0
PUBLICATION
- 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
- started implementing support for BiocParallel, allowing QuasR to also run on batch clusters
(support is currently limited to qQCReport)
QuasR 1.4.0
NEW FEATURES
- new arguments mapqMin and mapqMaxm in qCount, qProfile, qMeth and qExportWig allow to select alignments based on mapping quality
- qAlign gains checkOnly argument which allows checking for existing alignments without triggering new alignments in case of missing ones
QuasR 1.2.0
NEW FEATURES
- new miRNA-seq sample data; vignette has now workflows for ChIP-seq, RNA-seq, smRNA-seq/miRNA-seq, Bis-seq and allele-specific analysis
- qMeth can report methylation states for individual molecules (reportLevel="alignment")
- qCount/qProfile gain argument to ignore spliced reads in counting
QuasR 1.0.0
INITIAL RELEASE
- ChIP-seq with support for single-end, paired-end and allele specific samples
- RNA-seq with support for spliced alignment, single-end, paired-end and allele specific samples
- Bis-seq with support for single-end, paired-end and allele specific samples