https://github.com/arjunrajlaboratory/lost-in-space-public
public repository to recreate analyses in allelic correlation + noise transmission paper
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary
Repository
public repository to recreate analyses in allelic correlation + noise transmission paper
Basic Info
- Host: GitHub
- Owner: arjunrajlaboratory
- Language: MATLAB
- Default Branch: main
- Size: 332 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
lost-in-space-public
public repository to recreate analyses in allelic correlation + noise transmission paper
General
This code will generate all simulation data to replicate the analysis in the paper. However, despite using seeds for random number generation, small differences will likely arise from the data used in the paper. The generated data used in the paper is available at the dropbox link provided in the key resources table or upon request from the authors.
The limited data from Larsson et al. 2019 that was re-analyzed for the paper is provided in this repository and so does not need to be downloaded separately.
Usage
All scripts use relative path names and are made to be run from their directory.
To generate simulation data: Run /Data/GenerateDataScripts/alleleconstantsignal/Scripts/make* scripts then /Data/GenerateDataScripts/alleleconstantsignal/Scripts/save* scripts then /Data/GenerateDataScripts/alleleconstantsignal/Scripts/simulate* scripts
Warning, this will generate ~300GB of data and took ~4 weeks of computational time on a 2019 iMac with a 3GHz 6 core CPU and 40GB of RAM.
To analyze the simulated data, either run the above scripts or download the provided data from Dropbox and place into /Data/GenerateDataScripts/alleleconstantsignal/Data/
Then run /Data/GenerateDataScripts/alleleconstantsignal/Scripts/analyze* scripts
Finally, to recreate final analysis and plots, please run R scripts provided in /Paper/plotScripts
Citation
Please consider citing https://doi.org/10.1101/2021.11.26.470134
Owner
- Name: Arjun Raj's systems biology lab
- Login: arjunrajlaboratory
- Kind: organization
- Repositories: 40
- Profile: https://github.com/arjunrajlaboratory
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total 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
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