Package: sangeranalyseR
Type: Package
Title: sangeranalyseR: a suite of functions for the analysis of Sanger
        sequence data in R
Version: 1.20.0
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'
Config/pak/sysreqs: make libicu-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-18 06:31:12 UTC
RemoteUrl: https://github.com/bioc/sangeranalyseR
RemoteRef: RELEASE_3_22
RemoteSha: 8a55a58402acc6749ef79fdb1564d8f3bd1a927a
NeedsCompilation: no
Packaged: 2026-01-23 07:56:00 UTC; root
Built: R 4.5.2; ; 2026-01-23 07:57:44 UTC; windows
