clockSim: Streamlined Simulation of Circadian Gene Networks
A user-friendly workflow for simulating circadian clock gene networks. Despite decades of advances in modeling circadian clock dynamics, the lack of accessible tools for reproducible simulation workflows hinders the integration of computational modeling with experimental studies. 'clockSim' addresses this gap by providing models and helper functions with step-by-step vignettes. This package opens up system-level exploration of the circadian clock to wet-lab experimentalists, and future development will include additional clock architectures and other gene circuit models. Currently implemented models are based on Leloup and Goldbeter (1998) <doi:10.1177/074873098128999934>.
| Version: | 0.1.1 |
| Depends: | R (≥ 4.1.0) |
| Imports: | bench, dde, dplyr, ggplot2, lomb, matrixStats, odin, rlang, tidyr |
| Suggests: | knitr, rmarkdown |
| Published: | 2025-04-07 |
| DOI: | 10.32614/CRAN.package.clockSim |
| Author: | Ye Yuan  [aut,
cre, cph] |
| Maintainer: | Ye Yuan <yeyu at umich.edu> |
| BugReports: | https://github.com/yeyuan98/clockSim/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/yeyuan98/clockSim |
| NeedsCompilation: | yes |
| Materials: | NEWS |
| CRAN checks: | clockSim results |
Documentation:
| Reference manual: | clockSim.pdf |
| Vignettes: |
Simulation of the circadian clock (source, R code) Parameter grid scan to understand circadian clock model (source, R code) noisy-LG-model (source, R code) |
Downloads:
| Package source: | clockSim_0.1.1.tar.gz |
| Windows binaries: | r-devel: clockSim_0.1.1.zip, r-release: not available, r-oldrel: clockSim_0.1.1.zip |
| macOS binaries: | r-devel (arm64): clockSim_0.1.1.tgz, r-release (arm64): clockSim_0.1.1.tgz, r-oldrel (arm64): clockSim_0.1.1.tgz, r-devel (x86_64): clockSim_0.1.1.tgz, r-release (x86_64): clockSim_0.1.1.tgz, r-oldrel (x86_64): clockSim_0.1.1.tgz |
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