Reference

All functions
alignmentStats()	Get statistics on alignments
preprocessReads()	Preprocess Short Reads
qAlign()	Align reads
qCount()	Quantify alignments
qExportWig()	QuasR wig file export
qMeth()	Quantify DNA methylation
qProfile()	Quantify alignments by relative position
qProject-class show,qProject-method [,qProject,ANY,missing,missing-method alignments,qProject-method alignments auxiliaries,qProject-method auxiliaries genome,qProject-method length,qProject-method qProject class:qProject	qProject objects
qProjectUpdate()	Update qProject
qQCReport()	QuasR Quality Control Report