NEWS

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APAlyzer 1.9.4 (2022-02-28)

• Fixed typos in vignettes

APAlyzer 1.9.3 (2022-02-27)

• Fixed the issues caused by the lastest ensembl GRCm39 GTF.
• Fixed typos in vignettes

APAlyzer 1.9.2 (2022-01-02)

• Added supporting of multi-condition design in 'APAdiff'.

APAlyzer 1.9.1 (2021-11-28)

• Added 'MultiTest' parameter for APAdiff.
• Improved the performance and fixed issues in PAS2GEF.
• Update documents and authorships.

APAlyzer 1.7.3 (2021-08-01)

• Fixed the typo in vignettes.

APAlyzer 1.7.2 (2021-07-31)

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

APAlyzer 1.7.1 (2021-07-09)

• Fixed the missing SS column issues in PAS2GEF.

APAlyzer 1.5.5 (2021-01-31)

• Added ThreeMostPairBam to support paired-end bam.

APAlyzer 1.5.4 (2021-01-10)

• Fixed the bug in PASEXP_3UTR.

APAlyzer 1.5.3 (2021-01-05)

• Updated the link of PolyA_DB.

APAlyzer 1.5.1 (2020-12-07)

• Updated Imports and authors.

APAlyzer 1.3.3 (2020-07-20)

• Fixed hg38_REF.RData.

APAlyzer 1.3.2 (2020-07-20)

• Updated the CITATION.

APAlyzer 1.3.1 (2020-07-19)

• Fixed the interval issues in hg38_REF.RData and mm10_REF.RData.
• Updated the CITATION.

APAlyzer 1.1.3 (2020-04-27)

• Optimize code to reduce the testing time.

APAlyzer 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.

APAlyzer 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.

APAlyzer 1.1.0 (2020-02-27)

• Revise some typos in vignettes and mans.

APAlyzer 1.0.1 (2020-01-28)

• Revise some typos in vignettes and mans.

APAlyzer 0.99.2 (2019-08-18)

• Revise formats to consistent with Bioconductor coding styles.
• Added unit tests

APAlyzer 0.99.1 (2019-07-14)

• Submitted to Bioconductor