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: 1.32.1
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), dplyr (>= 0.7.2), data.table (>= 1.10.4-3),
        rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4)
RoxygenNote: 7.3.3
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' 'helpers_plots.R'
VignetteBuilder: knitr
Encoding: UTF-8
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-11-11 19:09:32 UTC
RemoteUrl: https://github.com/bioc/amplican
RemoteRef: RELEASE_3_22
RemoteSha: 91d4b741ff855f9bee4df3f19ccd736a05eaf3ae
NeedsCompilation: yes
Packaged: 2025-11-15 12:02:46 UTC; root
Author: Kornel Labun [aut],
  Eivind Valen [cph, cre]
Maintainer: Eivind Valen <eivind.valen@gmail.com>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-15 12:06:26 UTC; windows
Archs: x64
