DESCRIPTION

Package: sangeranalyseR
Type: Package
Title: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Version: 1.13.0
Date: 2020-04-22
Author: Rob Lanfear <rob.lanfear@gmail.com>, Kuan-Hao Chao <ntueeb05howard@gmail.com>
Maintainer: Kuan-Hao Chao <ntueeb05howard@gmail.com>
biocViews: Genetics, Alignment, Sequencing, SangerSeq, Preprocessing, 
           QualityControl, Visualization, GUI
Description: This package builds on sangerseqR to allow users to create contigs
             from collections of Sanger sequencing reads. It provides a wide 
             range of options for a number of commonly-performed actions 
             including read trimming, detecting secondary peaks, and detecting 
             indels using a reference sequence. All parameters can be adjusted 
             interactively either in R or in the associated Shiny applications. 
             There is extensive online documentation, and the package can outputs 
             detailed HTML reports, including chromatograms.
License: GPL-2
Encoding: UTF-8
Depends: 
    R (>= 4.0.0),
    stringr,
    ape,
    Biostrings,
    DECIPHER,
    parallel,
    reshape2,
    sangerseqR,
    gridExtra,
    shiny,
    shinydashboard,
    shinyjs,
    data.table,
    plotly,
    DT,
    zeallot,
    excelR,
    shinycssloaders,
    ggdendro,
    shinyWidgets,
    openxlsx,
    tools,
    rmarkdown (>= 2.9),
    knitr (>= 1.33),
    seqinr,
    BiocStyle,
    logger
RoxygenNote: 7.2.1
VignetteBuilder: knitr
Suggests: 
    testthat (>= 2.1.0)
Collate: 
    'AllGenerics.R'
    'ClassChromatogramParam.R'
    'ClassObjectResults.R'
    'ClassQualityReport.R'
    'ClassSangerRead.R'
    'ClassSangerAlignment.R'
    'ClassSangerContig.R'
    'Constructors.R'
    'LoadMessage.R'
    'MethodSangerAlignment.R'
    'MethodSangerContig.R'
    'MethodSangerRead.R'
    'MethodShared.R'
    'MethodsQualityReport.R'
    'ShinySangerAlignmentServer.R'
    'ShinySangerAlignmentUI.R'
    'ShinySangerContigServer.R'
    'ShinySangerContigUI.R'
    'ShinyServerModule.R'
    'UtilitiesFunc.R'
    'UtilitiesFuncInputChecker.R'
    'data.R'
    'sangeranalyseR_package.R'
    'sangeranalyseR_show_method.R'