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
Roxygen: list(markdown = TRUE)
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
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev zlib1g-dev
Repository: https://l-a-yates.r-universe.dev
Date/Publication: 2026-03-26 04:18:23 UTC
RemoteUrl: https://github.com/l-a-yates/cpam
RemoteRef: HEAD
RemoteSha: 9ebd3295f58cd1fb1bd97b8bcb5079df7eda42c6
NeedsCompilation: no
Packaged: 2026-10-11 13:00:31 UTC; root
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>