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. Changes in version 1.7.1 (2021-07-09) + Fixed the missing SS column issues in PAS2GEF. Changes in version 1.7.2 (2021-07-31) + Fixed the issues of using 3'most bam file (generate using ThreeMostPairBam) in PASEXP_IPA. Changes in version 1.7.3 (2021-08-01) + Fixed the typo in vignettes. Changes in version 1.9.1 (2021-11-28) + Added `MultiTest` parameter for APAdiff. + Improved the performance and fixed issues in PAS2GEF. + Update documents and authorships. Changes in version 1.9.2 (2022-01-02) + Added supporting of multi-condition design in `APAdiff`. Changes in version 1.9.3 (2022-02-27) + Fixed the issues caused by the lastest ensembl GRCm39 GTF. + Fixed typos in vignettes Changes in version 1.9.4 (2022-02-28) + Fixed typos in vignettes