Package: sangeranalyseR
Type: Package
Title: sangeranalyseR: a suite of functions for the analysis of Sanger
        sequence data in R
Version: 1.18.0
Date: 2024-04-24
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, pwalign, 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: 7.3.2
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'
git_url: https://git.bioconductor.org/packages/sangeranalyseR
git_branch: RELEASE_3_21
git_last_commit: b617df0
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 03:27:12 UTC; biocbuild
Built: R 4.5.0; ; 2025-04-16 15:29:55 UTC; windows
