Changes in version 1.8.0 NEW FEATURES o interest() and interest.sequential() functions support the possibility to define other parameter settings of BamFile() function of Rsamtools package e.g. "qnamePrefixEnd" and "qnameSuffixStart". o annotateU12() can return the PWM match scores (if requested). The hybrid AT-AG and GT-AC U12 types can be set to be ignored. The introns/exons coordinates can be filtered according to their map to another set of coordinates. BUG FIXES o referencePrepare() just gives warning and continue without annotating gene names (when annotateGeneIds=TRUE parameter is set) if annotating with gene names is not possible. o interest() used to return Error if single end mapped reads did not existed at all (despite being requetsed). This has been corrected. Changes in version 1.6.0 NEW FEATURES o buildSsTypePwms() function supports the possibility to select begin and end point of splice sites sequences from which PWMs are built. It also supports the possibility to paste splice sites to build PWM. BUG FIXES o interest.sequential() and interest(): corrections to their object output option. o annotateU12() modified to work correctly with the new changes in Biostrings package. o buildSsTypePwms() corrected and modified to better suit data for all species from SpliceRack and U12DB. Changes in version 1.4.0 NEW FEATURES o interest() and interest.sequential() functions now support "IntSpan" method, allows counting intron- spanning reads. o psi() function is added. It calculates Psi values. o annotateU12() fucntion supports DNAStringSet objects as its refGenome input. o Improved vignette document. SIGNIFICANT USER-VISIBLE CHANGES o eBayesInterest() removed. BUG FIXES o interest.sequential() and interest(): corrections to their object output option. o annotateU12() modified to work correctly with the new changes in Biostrings package.