Package: sangeranalyseR
Type: Package
Title: sangeranalyseR: a suite of functions for the analysis of Sanger
        sequence data in R
Version: 1.23.0
Date: 2024-04-24
Authors@R: c(
    person("Rob", "Lanfear", email = "rob.lanfear@gmail.com",
           role = "aut"),
    person("Kuan-Hao", "Chao", email = "ntueeb05howard@gmail.com",
           role = c("aut", "cre")))
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 | file LICENSE
URL: https://github.com/roblanf/sangeranalyseR
BugReports: https://github.com/roblanf/sangeranalyseR/issues
Encoding: UTF-8
Depends: R (>= 4.0.0), Biostrings, DECIPHER, sangerseqR
Imports: ape, BiocGenerics, BiocParallel, S4Vectors, data.table, DT,
        excelR, ggdendro, grDevices, graphics, gridExtra, logger,
        methods, openxlsx, parallel, plotly, pwalign, Rcpp, rmarkdown
        (>= 2.9), seqinr, shiny, shinycssloaders, shinydashboard,
        shinyjs, shinyWidgets, stats, stringr, tools, utils
LinkingTo: Rcpp
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Suggests: testthat (>= 2.1.0), withr, BiocManager, BiocStyle, knitr (>=
        1.33), reshape2, zeallot
Collate: 'AllGenerics.R' 'ClassChromatogramParam.R'
        'ClassObjectResults.R' 'ClassQualityReport.R'
        'ClassSangerRead.R' 'ClassSangerAlignment.R'
        'ClassSangerContig.R' 'Constructors.R' 'GlobalTrimApp.R'
        'LoadMessage.R' 'MethodSangerAlignment.R'
        'MethodSangerContig.R' 'MethodSangerRead.R' 'MethodShared.R'
        'MethodsQualityReport.R' 'RcppExports.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: cmake make libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-06 03:58:14 UTC
RemoteUrl: https://github.com/bioc/sangeranalyseR
RemoteRef: HEAD
RemoteSha: f6375aed24faaea28bd019d5c5fba4b8e47bcde1
NeedsCompilation: yes
Packaged: 2026-07-02 09:33:26 UTC; root
Author: Rob Lanfear [aut],
  Kuan-Hao Chao [aut, cre]
Maintainer: Kuan-Hao Chao <ntueeb05howard@gmail.com>