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>.
Version: 0.1.3 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) Published: 2025-03-13 DOI: 10.32614/CRAN.package.cpam Author: Luke Yates [aut, cre, cph], Michael Charleston [aut], Jazmine Humphreys [aut], Steven Smith [aut] Maintainer: Luke Yates <luke.yates at utas.edu.au> BugReports: https://github.com/l-a-yates/cpam/issues License: GPL (≥ 3) URL: https://l-a-yates.github.io/cpam/, https://github.com/l-a-yates/cpam NeedsCompilation: no Materials: README NEWS CRAN checks: cpam results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=cpam to link to this page.
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