Package: phiper
Title: Automated PhIP-seq Analysis and Reporting
Version: 0.4.1
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("ctb", "cph")
  ),
  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, readr, rmarkdown,
        rprojroot, testthat (>= 3.0.0), vdiffr, withr, yaml
VignetteBuilder: knitr
Config/testthat/edition: 3
Remotes: Polymerase3/phiperio
Imports: phiperio, chk, cli, DBI, dbplyr, dplyr, duckdb, ggplot2,
        rlang, scales, tibble, tidyr, tidyselect, vegan, Rcpp,
        RcppParallel, utils, Rtsne, plotly, showtext, sysfonts
Config/pak/sysreqs: cmake libfreetype6-dev make libicu-dev libpng-dev
        libuv1-dev libssl-dev xz-utils zlib1g-dev
Repository: https://polymerase3.r-universe.dev
Date/Publication: 2026-04-15 18:35:49 UTC
RemoteUrl: https://github.com/Polymerase3/phiper
RemoteRef: main
RemoteSha: 688367ea198d824e1db99e3025dfef7574553fdb
NeedsCompilation: yes
Packaged: 2026-06-14 08:13:57 UTC; root
Author: Mateusz Kolek [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-6470-4830>),
  Alon Alexander [ctb, cph],
  Thomas Vogl [cph, fnd] (ORCID: <https://orcid.org/0000-0002-3892-1740>)
Maintainer: Mateusz Kolek <mati.kolek13@gmail.com>