Package: InPAS
Title: A Bioconductor package for identifying novel Alternative
        PolyAdenylation Sites (PAS) from RNA-seq data
Version: 2.0.0
Authors@R: c(person("Jianhong", "Ou", role = c("aut", "cre"), 
             email = "jianhong.ou@duke.edu"), 
             person("Haibo", "Liu", role = c("aut"), 
             email = "haibo.liu@umassmed.edu"),
             person("Lihua Julie", "Zhu", role = c("aut"), 
             email = "Julie.Zhu@umassmed.edu"), 
             person("Sungmi M.", "Park", role = "aut"),
             person("Michael R.", "Green", role = "aut"))
Maintainer: Jianhong Ou <jianhong.ou@duke.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.
biocViews: RNASeq, Sequencing, AlternativeSplicing, Coverage,
        DifferentialSplicing, GeneRegulation, Transcription,
        ImmunoOncology
License: GPL (>= 2)
Imports: AnnotationDbi, BSgenome, cleanUpdTSeq, preprocessCore,
        IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel,
        Biostrings, dplyr, magrittr, plyranges, readr, RSQLite, DBI,
        purrr, GenomicFeatures, ggplot2, reshape2
Depends: R (>= 3.1), methods, Biobase, GenomicRanges, S4Vectors
Suggests: RUnit, BiocGenerics, BiocManager, rtracklayer, BiocStyle,
        knitr, markdown, rmarkdown, EnsDb.Hsapiens.v86,
        EnsDb.Mmusculus.v79, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Mmusculus.UCSC.mm10,
        TxDb.Hsapiens.UCSC.hg19.knownGene,
        TxDb.Mmusculus.UCSC.mm10.knownGene
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Roxygen: list(markdown = TRUE)
LazyData: true
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/InPAS
git_branch: RELEASE_3_13
git_last_commit: d402f5c
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: no
Packaged: 2021-05-20 00:28:59 UTC; biocbuild
Author: Jianhong Ou [aut, cre],
  Haibo Liu [aut],
  Lihua Julie Zhu [aut],
  Sungmi M. Park [aut],
  Michael R. Green [aut]
Built: R 4.1.0; ; 2021-05-20 14:22:46 UTC; unix
