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clockSim

R package for circadian clock gene network simulation

https://github.com/yeyuan98/clocksim

Science Score: 26.0%

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    CITATION.cff file
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    Found 1 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (8.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

R package for circadian clock gene network simulation

Basic Info
  • Host: GitHub
  • Owner: yeyuan98
  • License: gpl-3.0
  • Language: C
  • Default Branch: main
  • Size: 255 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Created about 1 year ago · Last pushed 11 months ago
Metadata Files
License

https://github.com/yeyuan98/clockSim/blob/main/ 

# clockSim



[![CRAN status](https://www.r-pkg.org/badges/version/clockSim)](https://CRAN.R-project.org/package=clockSim)
[![r-universe version](https://yeyuan98.r-universe.dev/clockSim/badges/version)](https://yeyuan98.r-universe.dev/clockSim)
[![r-universe status](https://yeyuan98.r-universe.dev/clockSim/badges/checks)](https://yeyuan98.r-universe.dev/clockSim)


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) .

## Installation

To install current CRAN version of clockSim:

``` r
install.packages("clockSim")
```

You can install the development version of clockSim from [GitHub](https://github.com/) with:

``` r
# install.packages("pak")
pak::pak("yeyuan98/clockSim")
```

## Usage

Refer to the package vignettes on example workflows on circadian clock simulation.

Owner

  • Name: Ye Yuan
  • Login: yeyuan98
  • Kind: user
  • Company: University of Michigan, Ann Arbor

GitHub Events

Total
  • Issues event: 3
  • Issue comment event: 1
  • Push event: 10
  • Pull request event: 1
  • Fork event: 1
  • Create event: 2
Last Year
  • Issues event: 3
  • Issue comment event: 1
  • Push event: 10
  • Pull request event: 1
  • Fork event: 1
  • Create event: 2

Packages

  • Total packages: 1
  • Total downloads:
    • cran 548 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: clockSim

Streamlined Simulation of Circadian Gene Networks

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 548 Last month
Rankings
Dependent packages count: 26.8%
Dependent repos count: 33.0%
Average: 48.9%
Downloads: 86.8%
Maintainers (1)
yeyu@umich.edu
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • bench * imports
  • dde * imports
  • dplyr * imports
  • ggplot2 * imports
  • lomb * imports
  • odin * imports
  • rlang * imports
  • tidyr * imports
  • knitr * suggests
  • rmarkdown * suggests