DOI: 10.18129/B9.bioc.InPAS  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see InPAS.

Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Bioconductor version: 3.16

Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.

Author: Jianhong Ou [aut, cre], Haibo Liu [aut], Lihua Julie Zhu [aut], Sungmi M. Park [aut], Michael R. Green [aut]

Maintainer: Jianhong Ou <jianhong.ou at>

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biocViews Alternative Polyadenylation, Differential Polyadenylation Site Usage, Gene Regulation, RNA-seq, Software, Transcription
Version 2.6.0
In Bioconductor since BioC 3.1 (R-3.2) (8 years)
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports AnnotationDbi, batchtools, Biobase, Biostrings, BSgenome, cleanUpdTSeq, depmixS4, dplyr, flock, future, future.apply, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, IRanges, limma, magrittr, methods, parallelly, plyranges, preprocessCore, readr, reshape2, RSQLite, stats, S4Vectors, utils
Suggests BiocGenerics, BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown, rmarkdown, rtracklayer, RUnit, grDevices, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene
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