Changes in version 0.99.1 (2019-07-14)
+ Submitted to Bioconductor
Changes in version 0.99.2 (2019-08-18)
+ Revise formats to consistent with Bioconductor coding styles.
+ Added unit tests
Changes in version 1.0.1 (2020-01-28)
+ Revise some typos in vignettes and mans.
Changes in version 1.1.0 (2020-02-27)
+ Revise some typos in vignettes and mans.
Changes in version 1.1.1 (2020-03-15)
+ Add the PAS2GEF to convert GTF to PAS reference.
+ Add the REF4PAS to generate reference region for both 3'UTR and introic PAS at the same time.
+ Add the APAVolcano and APABox to plot the APAdiff results.
+ Add Adjusted p-value option in APAdiff
+ Allow the user to set argument minMQS to filter minimum mapping quality score of counted reads.
+ Add the build-in PAS reference for hg38 and mm10.
+ Add the build-in PAS reference for all PASs including conserved and non-conserved.
+ Update vignettes and mans.
+ PAS reference regions are now moved to a separate repo.
Changes in version 1.1.2 (2020-03-18)
+ Add the download_testbam to download the testing data bam files.
+ Add extra section 'Complete Analysis Example' in vignettes
+ Revise some typos in vignettes and mans.
Changes in version 1.1.3 (2020-04-27)
+ Optimize code to reduce the testing time.
Changes in version 1.3.1 (2020-07-19)
+ Fixed the interval issues in hg38_REF.RData and mm10_REF.RData.
+ Updated the CITATION.
Changes in version 1.3.2 (2020-07-20)
+ Updated the CITATION.
Changes in version 1.3.3 (2020-07-20)
+ Fixed hg38_REF.RData.
Changes in version 1.5.1 (2020-12-07)
+ Updated Imports and authors.
Changes in version 1.5.3 (2021-01-05)
+ Updated the link of PolyA_DB.
Changes in version 1.5.4 (2021-01-10)
+ Fixed the bug in PASEXP_3UTR.
Changes in version 1.5.5 (2021-01-31)
+ Added ThreeMostPairBam to support paired-end bam.