Changes in version 1.25.2 (2026-04-05)                 

    o   Fixed compatibility with R-devel and Bioconductor 3.22/3.23.

    o   Fixed test failure caused by ggplot2 4.0+ S7 object type change.

    o   Replaced deprecated element_line(size=) with element_line(linewidth=).

    o   Replaced library(HybridMTest) calls with requireNamespace(); moved HybridMTest to Suggests.

    o   Migrated makeTxDbFromGRanges import from GenomicFeatures to txdbmaker.

    o   Added txdbmaker, rlang, and S4Vectors to Imports.

    o   Fixed undefined global variables (Print, queryHits, download.file, etc.).

    o   Added .Rbuildignore to exclude .travis.yml from build.

    o   Updated License field in DESCRIPTION.

                 Changes in version 1.9.4 (2022-02-28)                  

    o   Fixed typos in vignettes

                 Changes in version 1.9.3 (2022-02-27)                  

    o   Fixed the issues caused by the lastest ensembl GRCm39 GTF.

    o   Fixed typos in vignettes

                 Changes in version 1.9.2 (2022-01-02)                  

    o   Added supporting of multi-condition design in `APAdiff`.

                 Changes in version 1.9.1 (2021-11-28)                  

    o   Added `MultiTest` parameter for APAdiff.

    o   Improved the performance and fixed issues in PAS2GEF.

    o   Update documents and authorships.

                 Changes in version 1.7.3 (2021-08-01)                  

    o   Fixed the typo in vignettes.

                 Changes in version 1.7.2 (2021-07-31)                  

    o   Fixed the issues of using 3'most bam file (generate using ThreeMostPairBam) in PASEXP_IPA.

                 Changes in version 1.7.1 (2021-07-09)                  

    o   Fixed the missing SS column issues in PAS2GEF.

                 Changes in version 1.5.5 (2021-01-31)                  

    o   Added ThreeMostPairBam to support paired-end bam.

                 Changes in version 1.5.4 (2021-01-10)                  

    o   Fixed the bug in PASEXP_3UTR.

                 Changes in version 1.5.3 (2021-01-05)                  

    o   Updated the link of PolyA_DB.

                 Changes in version 1.5.1 (2020-12-07)                  

    o   Updated Imports and authors.

                 Changes in version 1.3.3 (2020-07-20)                  

    o   Fixed hg38_REF.RData.

                 Changes in version 1.3.2 (2020-07-20)                  

    o   Updated the CITATION.

                 Changes in version 1.3.1 (2020-07-19)                  

    o   Fixed the interval issues in hg38_REF.RData and mm10_REF.RData.

    o   Updated the CITATION.

                 Changes in version 1.1.3 (2020-04-27)                  

    o   Optimize code to reduce the testing time.

                 Changes in version 1.1.2 (2020-03-18)                  

    o   Add the download_testbam to download the testing data bam files.

    o   Add extra section 'Complete Analysis Example' in vignettes

    o   Revise some typos in vignettes and mans.

                 Changes in version 1.1.1 (2020-03-15)                  

    o   Add the PAS2GEF to convert GTF to PAS reference.

    o   Add the REF4PAS to generate reference region for both 3'UTR and introic PAS at the same time.

    o   Add the APAVolcano and APABox to plot the APAdiff results.

    o   Add Adjusted p-value option in APAdiff

    o   Allow the user to set argument minMQS to filter minimum mapping quality score of counted reads.

    o   Add the build-in PAS reference for hg38 and mm10.

    o   Add the build-in PAS reference for all PASs including conserved and non-conserved.

    o   Update vignettes and mans.

    o   PAS reference regions are now moved to a separate repo.

                 Changes in version 1.1.0 (2020-02-27)                  

    o   Revise some typos in vignettes and mans.

                 Changes in version 1.0.1 (2020-01-28)                  

    o   Revise some typos in vignettes and mans.

                 Changes in version 0.99.2 (2019-08-18)                 

    o   Revise formats to consistent with Bioconductor coding styles.

    o   Added unit tests

                 Changes in version 0.99.1 (2019-07-14)                 

    o   Submitted to Bioconductor