cpam: Changepoint Additive Models for Time Series Omics Data
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:
| Reference manual: | cpam.pdf |
| Vignettes: |
cpam (source, R code) |
Downloads:
| Package source: | cpam_0.1.3.tar.gz |
| Windows binaries: | r-devel: cpam_0.1.3.zip, r-release: not available, r-oldrel: cpam_0.1.3.zip |
| macOS binaries: | r-devel (arm64): cpam_0.1.3.tgz, r-release (arm64): cpam_0.1.3.tgz, r-oldrel (arm64): cpam_0.1.3.tgz, r-devel (x86_64): cpam_0.1.3.tgz, r-release (x86_64): cpam_0.1.3.tgz, r-oldrel (x86_64): cpam_0.1.3.tgz |
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