DESCRIPTION

Package: ScreenR
Type: Package
Title: Package to Perform High Throughput Biological Screening
Version: 0.99.55
Date: 2023-09-05 
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: 7.2.1
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'