Package: InPAS
Type: Package
Title: InPAS: a bioconductor package for the identification of novel
        alternative PolyAdenylation Sites (PAS) using RNA-seq data
Version: 1.18.0
Authors@R: c(person("Jianhong Ou", "Developer", role = c("aut", "cre"),
        email = "jianhong.ou@duke.edu"), person("Lihua Julie Zhu",
        "Developer", role = "aut", email = "Julie.Zhu@umassmed.edu"))
Author: Jianhong Ou, Sungmi M. Park, Michael R. Green and Lihua Julie Zhu
Maintainer: Jianhong Ou <jianhong.ou@duke.edu>,
 Lihua Julie Zhu <Julie.Zhu@umassmed.edu>
Description: 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.
biocViews: RNASeq, Sequencing, AlternativeSplicing, Coverage,
        DifferentialSplicing, GeneRegulation, Transcription,
        ImmunoOncology
License: GPL (>= 2)
Lazyload: yes
Imports: AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr,
        preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma,
        BiocParallel
Depends: R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures,
        S4Vectors
Suggests: RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/InPAS
git_branch: RELEASE_3_10
git_last_commit: 205b776
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: no
Packaged: 2019-10-30 03:07:37 UTC; biocbuild
Built: R 3.6.1; ; 2019-10-30 13:30:38 UTC; windows
