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: 1.30.0
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, data.table (>= 1.10.4-3)
Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>=
        1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.28.4),
        GenomeInfoDb (>= 1.12.2), BiocParallel (>= 1.10.1), gtable (>=
        0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>=
        3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>=
        3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>=
        0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4)
RoxygenNote: 7.3.1
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
git_url: https://git.bioconductor.org/packages/amplican
git_branch: RELEASE_3_21
git_last_commit: b1fcc5e
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-15 23:02:41 UTC; biocbuild
Author: Kornel Labun [aut],
  Eivind Valen [cph, cre]
Maintainer: Eivind Valen <eivind.valen@gmail.com>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 13:52:30 UTC; windows
Archs: x64
