DOI: 10.18129/B9.bioc.InPAS    

Identification of Novel alternative PolyAdenylation Sites (PAS)

Bioconductor version: Release (3.6)

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 from RNAseq data. It leverages cleanUpdTSeq to fine tune identified APA sites.

Author: Jianhong Ou, Sung Mi 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, RNASeq, Sequencing, Software, Transcription
Version 1.10.0
In Bioconductor since BioC 3.1 (R-3.2) (3 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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