Package: phiper
Title: Automated PhIP-seq Analysis and Reporting
Version: 0.4.20
Authors@R: c(
  person(
    "Mateusz", "Kolek", 
    email = "mati.kolek13@gmail.com", 
    role = c("aut", "cre", "cph"), 
    comment = c(ORCID = "0000-0001-6470-4830")
  ),
  person(
    "Alon", "Alexander",
    email = "a.alexander@umcg.nl",
    role = c("cph"),
    comment = "contributed code and shaped the package concept"
  ),
  person(
    "Nikolas", "Basler",
    email = "nikolas.basler@meduniwien.ac.at",
    role = c("ctb"),
    comment = c(ORCID = "0000-0003-0791-4369")
  ),
  person(
    "Thomas", "Vogl",
    email = "thomas.vogl@meduniwien.ac.at",
    role = c("cph", "fnd"),
    comment = c(ORCID = "0000-0002-3892-1740")
  )
  )
Description: Provides an end-to-end toolkit for Phage
        ImmunoPrecipitation- sequencing (PhIP-seq) data. Functions
        import raw peptide-sample count matrices, apply quality control
        filters, normalise library sizes, compute enrichment statistics
        and diversity metrics, and identify differentially enriched
        peptides or motifs. Results can be explored through tidy data
        frames, visualised with publication-ready ggplot2 graphics, or
        rendered into fully fledged HTML reports via R Markdown.
License: GPL (>= 3)
Depends: R (>= 4.1.0)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://github.com/Polymerase3/phiper,
        https://polymerase3.github.io/phiper/
BugReports: https://github.com/Polymerase3/phiper/issues
SystemRequirements: C++17
LinkingTo: Rcpp, RcppParallel
Suggests: future, future.apply, ggsignif, ggpubr, knitr, kableExtra,
        mgcv, mockery, openxlsx, parallelDist, plotly, readr,
        rmarkdown, rprojroot, Rtsne, testthat (>= 3.0.0), vdiffr,
        withr, yaml
VignetteBuilder: knitr
Config/testthat/edition: 3
Remotes: Polymerase3/phiperio
Imports: phiperio (>= 0.6.2), chk, DBI, dbplyr, dplyr, duckdb, ggplot2
        (>= 4.0.0), rlang, tibble, tidyr, vegan, Rcpp, RcppParallel,
        utils
Config/pak/sysreqs: cmake libicu-dev xz-utils
Repository: https://polymerase3.r-universe.dev
Date/Publication: 2026-10-19 06:13:50 UTC
RemoteUrl: https://github.com/Polymerase3/phiper
RemoteRef: main
RemoteSha: f393178d8ec6fad1b957652702b6a1f6964163bf
NeedsCompilation: yes
Packaged: 2026-10-19 06:44:52 UTC; root
Author: Mateusz Kolek [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-6470-4830>),
  Alon Alexander [cph] (contributed code and shaped the package concept),
  Nikolas Basler [ctb] (ORCID: <https://orcid.org/0000-0003-0791-4369>),
  Thomas Vogl [cph, fnd] (ORCID: <https://orcid.org/0000-0002-3892-1740>)
Maintainer: Mateusz Kolek <mati.kolek13@gmail.com>