Changes in version 2.18.1                        

    o   Remove plyranges::filter.

                       Changes in version 2.15.2                        

    o   Update email address.

                       Changes in version 2.15.1                        

    o   Add citation.

                        Changes in version 2.3.1                        

    o   merge changes made by Haibo.

                       Changes in version 1.99.4                        

    o   update get_PAscore2.

                       Changes in version 1.99.3                        

    o   add rmarkdown as suggests.

                       Changes in version 1.99.2                        

    o   fix a bug if utr3 list is empty.

                       Changes in version 1.99.1                        

    o   add dontrun for getGCandMappability doc.

                       Changes in version 1.99.0                        

    o   merge Haibo's code.

                       Changes in version 1.19.1                        

    o   replace all `class` by `is`.

                       Changes in version 1.17.3                        

    o   update documentation.

                       Changes in version 1.17.2                        

    o   add citation of cleanUpdTSeq.

                       Changes in version 1.15.2                        

    o   update author's email.

                       Changes in version 1.15.1                        

    o   add the new biocViews tag "ImmunoOncology"

                       Changes in version 1.11.4                        

    o   fix the warning for help files in windows

                       Changes in version 1.11.3                        

    o   add utr3.danRer10.

                       Changes in version 1.11.2                        

    o   fix the error by the change of GRanges.

                        Changes in version 1.7.5                        

    o   add Julie as co-maintainer.

                        Changes in version 1.7.4                        

BUG FIXES

    o   fix the bug if there is NA values for proximal site to be adjusted.

                        Changes in version 1.7.3                        

BUG FIXES

    o   remove the code modified from voom. And directly use diffSplice.

                        Changes in version 1.7.2                        

BUG FIXES

    o   Fix the memory trap if the dataset is huge when call CPsites.

                        Changes in version 1.7.1                        

BUG FIXES

    o   Fix the bug for empty bedgraph.

                        Changes in version 1.5.7                        

NEW FEATURE

    o   decrease the memory to run InPAS.

                        Changes in version 1.5.6                        

NEW FEATURE

    o   Add a parameter to control search the proximal site from both 
	direction or not.

                        Changes in version 1.5.5                        

NEW FEATURE

    o   search the proximal site from both direction.

                        Changes in version 1.5.4                        

NEW FEATURE

    o   Categorize novel distal events into "novel distal" and "truncated distal"

BUG FIXES

    o   fix the bug in proximalAdjByCleanUpdTSeq.

                        Changes in version 1.5.1                        

NEW FEATURE

    o   new function coverageRate for quality control.

BUG FIXES

    o   fix the error when not all the seqnames is in bedgraphs for CPsites.

                        Changes in version 1.3.2                        

BUG FIXES

    o   re-run coverage when worker is died for bpapply

                        Changes in version 1.3.1                        

    o   suppress the error not needed in phmm

                        Changes in version 1.1.9                        

    o   update documentation

                        Changes in version 1.1.8                        

BUG FIXES

    o   improve the distCP site search.

                        Changes in version 1.1.7                        

BUG FIXES

    o   typo "novel distal".

                        Changes in version 1.1.6                        

BUG FIXES

    o   fix the seqlevels style issue.

                        Changes in version 1.1.5                        

BUG FIXES

    o   improve limmaAnalyze algorithm

                        Changes in version 1.1.4                        

BUG FIXES

    o   improve the CP sites adjustment algorithm.

                        Changes in version 1.1.3                        

BUG FIXES

    o   shorten the CPU time of CP sites prediction

                        Changes in version 1.1.2                        

BUG FIXES

    o   update description

                        Changes in version 1.1.1                        

BUG FIXES

    o   fix the bug in FFT smooth when length of 3UTR is shorter than smooth power

                       Changes in version 0.99.7                        

NEW FEATURES

    o   compensation by last CDS but not by ratio.

                       Changes in version 0.99.6                        

BUG FIXES

    o   fix the bug in utr3UsageEstimation in calculating of PDUI

                       Changes in version 0.99.5                        

BUG FIXES

    o   fix the bug in utr3Annotation when multiple transcripts sharing same
	transcript name by Gviz::GeneRegionTrack

                       Changes in version 0.99.4                        

BUG FIXES

    o   fix the bug in documentation of utr3Annotation

                       Changes in version 0.99.3                        

BUG FIXES

    o   fix the output ranges from short form to whole 3UTR

                       Changes in version 0.99.2                        

BUG FIXES

    o   clear warnings when run check. 
	  Warning: multiple methods tables found for 'species'
	  Warning: multiple methods tables found for ‘organism’

                       Changes in version 0.99.1                        

BUG FIXES

    o   errors when run BioCheck. import all the package should be import.