Changes in version 1.26.0 SIGNIFICANT USER-VISIBLE CHANGES o IntSpan method is changed to count reads that span the whole intron precisely. Previous these were counted separayted for 5' end and 3' end of the introns. o repeatsTableToFilter is ignored for IntSpana nd ExSkip as the skipped regions of the reads (denoted by N or sometimes D in the CIGAR of bam/sam file ) are taken into count for these benchmarks (not the mapped regions which are dentoed with Ms in the cigar). Changes in version 1.24.0 NEW FEATURES o strandSpecific is a new parameter added to interest() and interest.sequential(). It indicates that IntEREst is now strand-aware. All analysis can be run whilst taking into account (or ignoring) the strand specificity of the sequencing reads. o referencePrepare can create references (with collapsed exons) that does not ignore the strand information. SIGNIFICANT USER-VISIBLE CHANGES o GenomicFiles::reduceByYield function is now used instead of BiocParallel::bpiterat for improved efficiency and readability. This relates to how analysis related to different pieces of the alignment data is distributed over the parallel cores and the results are sumarized. BUG FIXES o In interest() and and interest.sequential() The oredr of the results of the different methods in the result matrix is corrected. Correct running of analyses using multiple methods with a single command is now possible. Changes in version 1.22.0 NEW FEATURES o method parameter in interest() and interest.sequential() functions now support "ExSkip". For each exon, the fucntions can now count the number of reads that skip over the exons. Changes in version 1.20.0 NEW FEATURES o limitRanges parameter in interest() and interest.sequential() functions allow for targetted analysis. It only loads reads that map to the defined coordinates. Changes in version 1.12.0 BUG FIXES o Replacing class( x ) == "foo" with is( x , "foo") . Changes in version 1.10.0 NEW FEATURES o applyOverlap() Apply a function on counts of a SummarizedExperiment basd on the overlaps of its genome coordinates to with another SummarizedExperiment. BUG FIXES o referencePrepare() stopped from modifying chromosome names.I doesn't add "chr" to the beginning of chromosome names. 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.