Package: PhIPData
Type: Package
Title: Container for PhIP-Seq Experiments
Version: 1.11.0
Authors@R: c(person("Athena", "Chen", email = "achen70@jhu.edu", 
    role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6900-2264")),
    person("Rob", "Scharpf", email = "rscharpf@jhu.edu", 
    role = c("aut")), 
    person("Ingo", "Ruczinski", email = "ingo@jhu.edu", 
    role = c("aut")))
Description: PhIPData defines an S4 class for phage-immunoprecipitation 
    sequencing (PhIP-seq) experiments. Buliding upon the 
    RangedSummarizedExperiment class, PhIPData enables users to coordinate 
    metadata with experimental data in analyses. Additionally, PhIPData 
    provides specialized methods to subset and identify beads-only samples, 
    subset objects using virus aliases, and use existing peptide libraries to 
    populate object parameters. 
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
Depends: 
    R (>= 4.1.0), 
    SummarizedExperiment (>= 1.3.81)
Imports:
    BiocFileCache,
    BiocGenerics, 
    methods, 
    GenomicRanges, 
    IRanges,
    S4Vectors, 
    edgeR,
    cli, 
    utils
Suggests:
    BiocStyle, 
    testthat,
    knitr,
    rmarkdown,
    covr, 
    dplyr,
    readr, 
    withr
biocViews: Infrastructure, DataRepresentation, Sequencing, Coverage
BugReports: https://github.com/athchen/PhIPData/issues
Collate: 
    'defineBeads.R'
    'PhIPData-class.R'
    'alias.R'
    'library.R'
    'subset.R'
    'summaries.R'
    'zzz.R'
RoxygenNote: 7.1.2
VignetteBuilder: knitr