NEWS

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InPAS 2.3.1

• merge changes made by Haibo.

InPAS 1.99.4

• update get_PAscore2.

InPAS 1.99.3

• add rmarkdown as suggests.

InPAS 1.99.2

• fix a bug if utr3 list is empty.

InPAS 1.99.1

• add dontrun for getGCandMappability doc.

InPAS 1.99.0

• merge Haibo's code.

InPAS 1.19.1

• replace all 'class' by 'is'.

InPAS 1.17.3

• update documentation.

InPAS 1.17.2

• add citation of cleanUpdTSeq.

InPAS 1.15.2

• update author's email.

InPAS 1.15.1

• add the new biocViews tag "ImmunoOncology"

InPAS 1.11.4

• fix the warning for help files in windows

InPAS 1.11.3

• add utr3.danRer10.

InPAS 1.11.2

• fix the error by the change of GRanges.

InPAS 1.7.5

• add Julie as co-maintainer.

InPAS 1.7.4

BUG FIXES

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

InPAS 1.7.3

BUG FIXES

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

InPAS 1.7.2

BUG FIXES

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

InPAS 1.7.1

BUG FIXES

• Fix the bug for empty bedgraph.

InPAS 1.5.7

NEW FEATURE

• decrease the memory to run InPAS.

InPAS 1.5.6

NEW FEATURE

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

InPAS 1.5.5

NEW FEATURE

• search the proximal site from both direction.

InPAS 1.5.4

NEW FEATURE

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

BUG FIXES

• fix the bug in proximalAdjByCleanUpdTSeq.

InPAS 1.5.1

NEW FEATURE

• new function coverageRate for quality control.

BUG FIXES

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

InPAS 1.3.2

BUG FIXES

• re-run coverage when worker is died for bpapply

InPAS 1.3.1

• suppress the error not needed in phmm

InPAS 1.1.9

• update documentation

InPAS 1.1.8

BUG FIXES

• improve the distCP site search.

InPAS 1.1.7

BUG FIXES

• typo "novel distal".

InPAS 1.1.6

BUG FIXES

• fix the seqlevels style issue.

InPAS 1.1.5

BUG FIXES

• improve limmaAnalyze algorithm

InPAS 1.1.4

BUG FIXES

• improve the CP sites adjustment algorithm.

InPAS 1.1.3

BUG FIXES

• shorten the CPU time of CP sites prediction

InPAS 1.1.2

BUG FIXES

• update description

InPAS 1.1.1

BUG FIXES

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

InPAS 0.99.7

NEW FEATURES

• compensation by last CDS but not by ratio.

InPAS 0.99.6

BUG FIXES

• fix the bug in utr3UsageEstimation in calculating of PDUI

InPAS 0.99.5

BUG FIXES

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

InPAS 0.99.4

BUG FIXES

• fix the bug in documentation of utr3Annotation

InPAS 0.99.3

BUG FIXES

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

InPAS 0.99.2

BUG FIXES

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

InPAS 0.99.1

BUG FIXES

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