cpam: Changepoint Additive Models for Time Series Omics Data (original) (raw)
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 |
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