DOI: 10.18129/B9.bioc.InPAS    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see InPAS.

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Bioconductor version: 3.11

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 due to internal-priming.

Author: Jianhong Ou, Sungmi M. Park, Michael R. Green and Lihua Julie Zhu

Maintainer: Jianhong Ou <jianhong.ou at>, Lihua Julie Zhu <Julie.Zhu at>

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biocViews AlternativeSplicing, Coverage, DifferentialSplicing, GeneRegulation, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version 1.20.0
In Bioconductor since BioC 3.1 (R-3.2) (5.5 years)
License GPL (>= 2)
Depends R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures, S4Vectors
Imports AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr, preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel
Suggests RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10,,, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr
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