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.