Package: mutscan
Title: Preprocessing and Analysis of Deep Mutational Scanning Data
Version: 1.0.0
Authors@R: 
    c(person(given = "Charlotte",
             family = "Soneson",
             role = c("aut", "cre"),
             email = "charlottesoneson@gmail.com",
             comment = c(ORCID = "0000-0003-3833-2169")),
      person(given = "Michael",
    	       family = "Stadler",
    	       role = c("aut"),
    	       email = "michael.stadler@fmi.ch",
    	       comment = c(ORCID = "0000-0002-2269-4934")),
      person(given = "Friedrich Miescher Institute for Biomedical Research",
             role = "cph"))
Description: Provides functionality for processing and statistical analysis 
    of multiplexed assays of variant effect (MAVE) and similar data. The 
    package contains functions covering the full workflow from raw FASTQ 
    files to publication-ready visualizations. A broad range of library 
    designs can be processed with a single, unified interface. 
Depends: R (>= 4.5.0)
Imports: BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp,
        edgeR (>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally,
        ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw,
        rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray,
        tools
Suggests: testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign,
        plotly, scattermore, BiocManager
SystemRequirements: GNU make
biocViews: GeneticVariability, GenomicVariation, Preprocessing
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
LinkingTo: Rcpp
Config/testthat/edition: 3
URL: https://github.com/fmicompbio/mutscan
BugReports: https://github.com/fmicompbio/mutscan/issues
git_url: https://git.bioconductor.org/packages/mutscan
git_branch: RELEASE_3_22
git_last_commit: 79672e3
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: yes
Packaged: 2025-10-30 05:22:40 UTC; biocbuild
Author: Charlotte Soneson [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3833-2169>),
  Michael Stadler [aut] (ORCID: <https://orcid.org/0000-0002-2269-4934>),
  Friedrich Miescher Institute for Biomedical Research [cph]
Maintainer: Charlotte Soneson <charlottesoneson@gmail.com>
