DESCRIPTION

Package: APAlog
Title: Analysis of alternative poly A site usage
Version: 0.99.0
Authors@R:
    c(person(given = "Hossein",
           family = "Asgharian",
           role = c("aut"),
           email = "hossein.asgharian@gmail.com",
           comment = c(ORCID = "https://orcid.org/0000-0001-7085-5045")),
    person(given = "Sohit",
           family = "Miglani",
           role = c("cre"),
           email = "sohitmiglani@gmail.com",
           comment = c(ORCID = "https://orcid.org/0000-0002-8075-320X")))
Description: Many trancripts in human and other organisms have multiple potential poly A sites.
  Selection of different poly A sites affects the composition of 3' UTR and the the regulatory elements it contains,
  and may impact several aspects of mRNA life cycle e.g. stability and translation rate. The APAlog package tests
  the significance of differential poly A site usage for each transcript across samples. The source of input data
  can be a 3' sequencing protocol e.g. Tag-Seq or QuantSeq, or regular RNA-seq with an annotation file.
  Three modes of analysis are offered: Overall transcript-wise test to evaluate the existence of differential pA usage,
  pairwise comparison of all pA sites of a transcript, or setting one pA site as the canonical or reference site
  and comparing every other pA site to this reference.
URL: https://github.com/goodarzilab/APAlog
BugReports: https://github.com/goodarzilab/APAlog/issues
License: MIT
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends:
    R (>= 4.0)
Imports:
    data.table,
    nnet,
    plyr,
    utils,
    EnhancedVolcano,
    qvalue
Suggests:
    knitr
biocViews:
    BiomedicalInformatics,
    DataImport,
    Software,
    ComparativeGenomics,
    GeneExpression,
    DifferentialExpression,
    Genetics,
    SystemsBiology,
    Sequencing,
    MultipleComparison
VignetteBuilder:
    knitr