Package: amplican
Type: Package
Title: Automated analysis of CRISPR experiments
Description: `amplican` performs alignment of the amplicon reads,
        normalizes gathered data, calculates multiple statistics (e.g.
        cut rates, frameshifts) and presents results in form of
        aggregated reports. Data and statistics can be broken down by
        experiments, barcodes, user defined groups, guides and
        amplicons allowing for quick identification of potential
        problems.
Version: 1.35.4
Authors@R: c(
    person("Kornel", "Labun", email = "kornel.labun@gmail.com", role = "aut"),
    person("Eivind", "Valen", email = "eivind.valen@gmail.com", role = c("cph", "cre"))
  )
URL: https://github.com/valenlab/amplican
BugReports: https://github.com/valenlab/amplican/issues
biocViews: ImmunoOncology, Technology, Alignment, qPCR, CRISPR
License: GPL-3
LinkingTo: Rcpp
Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings
        (>= 2.44.2), pwalign
Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>=
        1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.61.1),
        Seqinfo, BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra
        (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), stringr
        (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix
        (>= 1.2-10), data.table (>= 1.10.4-3), rmarkdown (>= 1.6),
        knitr (>= 1.16), cluster (>= 2.1.4), rlang (>= 1.2.0)
Suggests: testthat, BiocStyle, GenomicAlignments
Collate: 'helpers_general.R' 'AlignmentsExperimentSet-class.R'
        'RcppExports.R' 'helpers_rmd.R' 'amplicanReport.R'
        'helpers_directory.R' 'helpers_warnings.R' 'helpers_filters.R'
        'helpers_alignment.R' 'amplicanAlign.R' 'amplican.R'
        'amplicanFilter.R' 'amplicanNormalize.R' 'amplicanSummarize.R'
        'ggforce_bezier.R' 'globals.R' 'helpers_plots.R'
VignetteBuilder: knitr
Encoding: UTF-8
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev libjpeg-dev
        liblzma-dev libpng-dev libuv1-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-17 10:07:01 UTC
RemoteUrl: https://github.com/bioc/amplican
RemoteRef: HEAD
RemoteSha: c3ec0014bc75ff2588700f0ec1a3868d174803b2
NeedsCompilation: yes
Packaged: 2026-06-17 11:51:27 UTC; root
Author: Kornel Labun [aut],
  Eivind Valen [cph, cre]
Maintainer: Eivind Valen <eivind.valen@gmail.com>