Package: cpam
Title: Changepoint Additive Models for Time Series Omics Data
Version: 0.2.1
Authors@R: 
  c(person("Luke", "Yates", email = "luke.yates@utas.edu.au", role = c("aut", "cre","cph"),
  comment = c(ORCID = "0000-0002-1685-3169")),
  person("Michael", "Charleston", role = "aut"),
  person("Jazmine", "Humphreys", role = "aut"),
  person("Steven", "Smith", role = "aut"))
Description: Provides a comprehensive framework for time series omics analysis,
  integrating changepoint detection, smooth and shape-constrained trends,
  and uncertainty quantification. It supports gene- and transcript-level inferences,
  p-value aggregation for improved power, and both case-only and case-control designs.
  It includes an interactive 'shiny' interface. The methods are described in Yates et al. (2024) <doi:10.1101/2024.12.22.630003>.
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
Imports: bslib, cli, dplyr, edgeR, ggplot2, grDevices, magrittr,
        matrixStats, mgcv, mvnfast, parallel, pbmcapply, purrr,
        RColorBrewer, rlang, scam, shiny, shinyjs, stats, stringr,
        tidyr, tximport
Depends: R (>= 3.5)
URL: https://l-a-yates.github.io/cpam/,
        https://github.com/l-a-yates/cpam
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
BugReports: https://github.com/l-a-yates/cpam/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-03-26 23:40:14 UTC; layates
Author: Luke Yates [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-1685-3169>),
  Michael Charleston [aut],
  Jazmine Humphreys [aut],
  Steven Smith [aut]
Maintainer: Luke Yates <luke.yates@utas.edu.au>
Repository: CRAN
Date/Publication: 2026-03-27 00:30:02 UTC
Built: R 4.6.1; ; 2026-06-25 03:42:07 UTC; windows
