Package: InPAS
Title: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
Version: 2.19.1
Authors@R: c(person("Jianhong", "Ou", role = c("aut", "cre"), 
             email = "jou@morgridge.org"), 
             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 <jou@morgridge.org>
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: Alternative Polyadenylation, Differential Polyadenylation Site Usage, 
           RNA-seq, Gene Regulation, Transcription
License: GPL (>= 2)
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, Seqinfo, stats,
         S4Vectors, utils
Depends: R (>= 3.5)
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
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE)
LazyData: true
Encoding: UTF-8
git_url: https://git.bioconductor.org/packages/InPAS
git_branch: devel
git_last_commit: f16f642
git_last_commit_date: 2025-11-20
Repository: Bioconductor 3.23
