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 |