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: |
0.2.0 |
| 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: |
2026-03-04 |
| 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 |