Package: sangeranalyseR
Type: Package
Title: sangeranalyseR: a suite of functions for the analysis of Sanger
        sequence data in R
Version: 1.2.0
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, phangorn, sangerseqR, gridExtra, shiny,
        shinydashboard, shinyjs, data.table, plotly, DT, zeallot,
        excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx,
        tools, rmarkdown, kableExtra, seqinr, BiocStyle, logger
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Suggests: knitr, testthat (>= 2.1.0)
Collate: 'AllGenerics.R' 'ClassChromatogramParam.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'
git_url: https://git.bioconductor.org/packages/sangeranalyseR
git_branch: RELEASE_3_13
git_last_commit: 1dc9873
git_last_commit_date: 2021-05-19
Date/Publication: 2021-05-19
NeedsCompilation: no
Packaged: 2021-05-19 22:43:22 UTC; biocbuild
Built: R 4.1.0; ; 2021-06-01 23:04:08 UTC; unix
