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.