Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: nature.com -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.7%) to scientific vocabulary
Keywords
Repository
sRACIPE for bioconductor
Basic Info
- Host: GitHub
- Owner: vivekkohar
- License: mit
- Language: R
- Default Branch: master
- Homepage: https://www.nature.com/articles/s41540-018-0076-x
- Size: 7.8 MB
Statistics
- Stars: 0
- Watchers: 0
- Forks: 1
- Open Issues: 1
- Releases: 0
Topics
Metadata Files
README.md
sRACIPE
Stochastic analysis for Random Circuit Perturbation
sRACIPE implements a randomization-based method for gene circuit modeling. It allows us to study the effect of both the gene expression noise and the parametric variation on any gene regulatory circuit (GRC) using only its topology, and simulates an ensemble of models with random kinetic parameters at multiple noise levels. Statistical analysis of the generated gene expressions reveals the basin of attraction and stability of various phenotypic states and their changes associated with intrinsic and extrinsic noises. sRACIPE provides a holistic picture to evaluate the effects of both the stochastic nature of cellular processes and the parametric variation.
If you use sRACIPE, please consider citing our paper Role of noise and parametric variation in the dynamics of gene regulatory circuits published in npj Systems Biology and Applications.
Installation
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sRACIPE")
Or install the github version for new features. This will allow installation of most recent sRACIPE even if you are using older R and Bioconductor.
library(devtools)
install_github(“vivekkohar/sRACIPE”)
Build Reports
– Bioconductor Release
– Bioconductor devel
Owner
- Name: Vivek Kohar
- Login: vivekkohar
- Kind: user
- Website: http://vivekkohar.github.io/
- Repositories: 2
- Profile: https://github.com/vivekkohar
GitHub Events
Total
- Issue comment event: 1
Last Year
- Issue comment event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Vivek Kohar | v****r@g****m | 32 |
| Nitesh Turaga | n****a@g****m | 4 |
| Vivek Kohar | v****r@V****l | 3 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- LalicJ (1)
Pull Request Authors
- vivekkohar (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 10,222 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: sRACIPE
Systems biology tool to simulate gene regulatory circuits
- Homepage: https://github.com/lusystemsbio/sRACIPE https://geneex.jax.org/ https://vivekkohar.github.io/sRACIPE/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/sRACIPE/inst/doc/sRACIPE.pdf
- License: MIT + file LICENSE
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Latest release: 2.0.1
published 9 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6.0 depends
- Rcpp * depends
- SummarizedExperiment * depends
- methods * depends
- BiocGenerics * imports
- MASS * imports
- RColorBrewer * imports
- S4Vectors * imports
- ggplot2 * imports
- gplots * imports
- grDevices * imports
- graphics * imports
- gridExtra * imports
- htmlwidgets * imports
- reshape2 * imports
- stats * imports
- umap * imports
- utils * imports
- visNetwork * imports
- BiocStyle * suggests
- doFuture * suggests
- knitr * suggests
- rmarkdown * suggests
- tinytest * suggests