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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 ORCID iD [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: not available, 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

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.