Changepoint Additive Models for Time Series Omics Data R package cpam version 0.2.1 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>. Software Depends: R (>= 3.5) Imports: bslib, cli, dplyr, edgeR, ggplot2, grDevices, magrittr, matrixStats, mgcv, mvnfast, parallel, pbmcapply, purrr, RColorBrewer, rlang, scam, shiny, shinyjs, stats, stringr, tidyr, tximport Suggests: knitr, rmarkdown, testthat (>= 3.0.0) Luke Yates <luke.yates@utas.edu.au> Comprehensive R Archive Network (CRAN) Luke Yates [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-1685-3169>), Michael Charleston [aut], Jazmine Humphreys [aut], Steven Smith [aut] GPL (>= 3) 2026-03-27 application/tgz https://CRAN.R-project.org/package=cpam doi:10.32614/CRAN.package.cpam