Package: ScreenR
Type: Package
Title: Package to Perform High Throughput Biological Screening
Version: 1.11.0
Date: 2022-04-01
Authors@R: c(person("Emanuel Michele", "Soda", role = c("aut", "cre"),
                  email = "emanuelsoda@gmail.com", 
                  comment = c(ORICD = "0000-0002-2301-6465")),
            person("Elena", "Ceccacci", role = c("aut"),
                   email = "elena.ceccacci@ieo.it", 
                   comment = c(ORICD = "0000-0002-2285-8994")),
            person("Saverio", "Minucci", role = c("fnd", "ths"),
                   email = "saverio.minucci@ieo.it", 
                   comment = c(ORICD = "0000-0001-5678-536X")))
Description: ScreenR is a package suitable to perform hit identification in loss 
            of function High Throughput Biological Screenings performed using 
            barcoded shRNA-based  libraries. ScreenR combines the computing 
            power of software such as  edgeR with the simplicity of use of the 
            Tidyverse metapackage. ScreenR executes a pipeline able to find 
            candidate hits from barcode counts, and integrates a wide range of 
            visualization modes for each step of the analysis.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.2.0
Imports: methods (>= 4.0), rlang (>= 0.4), stringr (>= 1.4), limma (>=
        3.46), patchwork (>= 1.1), tibble (>= 3.1.6), scales (>=
        1.1.1), ggvenn (>= 0.1.9), purrr (>= 0.3.4), ggplot2 (>= 3.3),
        stats, tidyr (>= 1.2), magrittr (>= 1.0), dplyr (>= 1.0), edgeR
        (>= 3.32), tidyselect (>= 1.1.2)
Suggests: rmarkdown (>= 2.11), knitr (>= 1.37), testthat (>= 3.0.0),
        BiocStyle (>= 2.22.0), covr (>= 3.5)
Config/testthat/edition: 3
Depends: R (>= 4.2)
VignetteBuilder: knitr
biocViews: Software, AssayDomain, GeneExpression
BugReports: https://github.com/EmanuelSoda/ScreenR/issues
URL: https://emanuelsoda.github.io/ScreenR/
Collate: 'ScreenR-package.R' 'annotation_table.R' 'barcode_lost.R'
        'camera_method.R' 'compute_data_table.R' 'compute_metrics.R'
        'count_mapped_reads.R' 'count_table.R' 'create_object.R'
        'distribution_mapped_reads.R' 'filter_by.R' 'find_common_hit.R'
        'find_roast_hit.R' 'find_robust_zscore_hit.R'
        'find_zscore_hit.R' 'generics.R' 'mapped_reads.R'
        'normalize_data.R' 'plot_barcode_hit.R' 'plot_barcode_trend.R'
        'plot_boxplot.R' 'plot_mapped_reads.R' 'plot_mds.R'
        'plot_trend.R' 'plot_zscore_distribution.R' 'screenr-class.R'
        'zzz.R'
git_url: https://git.bioconductor.org/packages/ScreenR
git_branch: devel
git_last_commit: 8f08b42
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 02:00:18 UTC; biocbuild
Author: Emanuel Michele Soda [aut, cre] (ORICD: 0000-0002-2301-6465),
  Elena Ceccacci [aut] (ORICD: 0000-0002-2285-8994),
  Saverio Minucci [fnd, ths] (ORICD: 0000-0001-5678-536X)
Maintainer: Emanuel Michele Soda <emanuelsoda@gmail.com>
Built: R 4.5.0; ; 2025-06-05 13:59:34 UTC; windows
