Package: clockSim 0.1.2

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>.

Authors:Ye Yuan [aut, cre, cph]

clockSim_0.1.2.tar.gz
clockSim_0.1.2.zip(r-4.7)clockSim_0.1.2.zip(r-4.6)clockSim_0.1.2.zip(r-4.5)
clockSim_0.1.2.tgz(r-4.6-x86_64)clockSim_0.1.2.tgz(r-4.6-arm64)clockSim_0.1.2.tgz(r-4.5-x86_64)clockSim_0.1.2.tgz(r-4.5-arm64)
clockSim_0.1.2.tar.gz(r-4.7-arm64)clockSim_0.1.2.tar.gz(r-4.7-x86_64)clockSim_0.1.2.tar.gz(r-4.6-arm64)clockSim_0.1.2.tar.gz(r-4.6-x86_64)
clockSim_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
clockSim/json (API)

# Install 'clockSim' in R:
install.packages('clockSim', repos = c('https://yeyuan98.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yeyuan98/clocksim/issues

On CRAN:

Conda:

3.18 score 1 stars 4 scripts 67 downloads 9 exports 75 dependencies

Last updated from:1afb7d2e51. Checks:11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING149
linux-devel-x86_64WARNING153
source / vignettesOK271
linux-release-arm64WARNING152
linux-release-x86_64WARNING145
macos-release-arm64WARNING102
macos-release-x86_64WARNING153
macos-oldrel-arm64WARNING116
macos-oldrel-x86_64WARNING220
windows-develWARNING95
windows-releaseWARNING135
windows-oldrelWARNING110
wasm-releaseOK130

Exports:compute_cosinecompute_normalizecompute_periodcompute_rmsegetOdinGengrid_scanplot_phaseplot_timeSeriesrun_eta

Dependencies:askpassbase64encbenchbslibcachemcinterpolateclicpp11crosstalkcurldata.tableddedeSolvedigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlazyevallifecyclelombmagrittrmatrixStatsmemoisemimeodinopensslotelpillarpkgconfigplotlypracmaprofmempromisespurrrR6rappdirsRColorBrewerRcppringrlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml

Scanning parameter grid to understand circadian clock model
Baseline: a limit cycle oscillator | Initial state grid scan | Grid generation | Running grid_scan()
Rendered fromgrid-scan.Rmdusingknitr::rmarkdown

Last update: 2025-03-28
Started: 2025-02-22

Models for circadian clock simulation
LG model simulation scheme | Continuous LG model | Discrete LG model | Discrete LG model: how small time step is enough?
Rendered fromclock-models.Rmdusingknitr::rmarkdown

Last update: 2025-03-23
Started: 2025-02-22

Noisy LG model: incorporating noise to the classical LG ODE clock model
A SDE LG model | When is the model valid? | Noising scaling | Loading the noisy LG model | Example: noise in tim RNA M_T turnover | Phase portrait and periodogram
Rendered fromnoisy-LG-model.Rmdusingknitr::rmarkdown

Last update: 2025-03-09
Started: 2025-03-09