Changes in version 1.25.2 (2026-04-05)
+ Fixed compatibility with R-devel and Bioconductor 3.22/3.23.
+ Fixed test failure caused by ggplot2 4.0+ S7 object type change.
+ Replaced deprecated element_line(size=) with element_line(linewidth=).
+ Replaced library(HybridMTest) calls with requireNamespace(); moved HybridMTest to Suggests.
+ Migrated makeTxDbFromGRanges import from GenomicFeatures to txdbmaker.
+ Added txdbmaker, rlang, and S4Vectors to Imports.
+ Fixed undefined global variables (Print, queryHits, download.file, etc.).
+ Added .Rbuildignore to exclude .travis.yml from build.
+ Updated License field in DESCRIPTION.
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