版本0.99.1(2019-07-14)的变更+提交给Bioconductor版本0.99.2(2019-08-18)的变更+修改格式以与Bioconductor编码风格一致。+增加了单元测试版本1.0.1(2020-01-28)的更改+修改了小插图和man中的一些拼写错误。版本1.1.0(2020-02-27)的变更+修改小插图和文字中的一些拼写错误。版本1.1.1(2020-03-15)更改+添加PAS2GEF以将GTF转换为PAS引用。+添加REF4PAS，同时生成3'UTR和intric PAS的参考区域。+添加ap火山和APABox绘制APAdiff结果。+在APAdiff中添加调整后的p值选项+允许用户设置参数minMQS来过滤已计数读取的最小映射质量分数。+添加hg38和mm10的内置PAS参考。+为所有PASs(包括保守和非保守)添加内置PAS参考。+更新小插图和男人。 + 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