exp-growth
Time-series methods for disease-agnostic metagenomic environmental threat detection
Science Score: 31.0%
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Low similarity (4.7%) to scientific vocabulary
Repository
Time-series methods for disease-agnostic metagenomic environmental threat detection
Basic Info
- Host: GitHub
- Owner: athowes
- License: mit
- Language: R
- Default Branch: master
- Homepage: https://athowes.github.io/exp-growth
- Size: 132 MB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
exp-growth
This repository contains work I did over June - August 2022 at the Nucleic Acid Observatory, MIT Media Lab. My focus was primarily on computational threat detection of emerging pandemics using exponential growth detection of environmental metagenomic data. Poisson regression works well for this in easy simulated cases, and it remains to be seen for more realistic ones. See:
- Poisson regression as an approach to exponential growth detection
- Estimating exponential growth via sporadic detection
- Exponential growth detection on metagenomic data
I also began developing a Bayesian generative model for qPCR, modelling the amplification curve rather than only $C_t$. Why? Emerging pathogens will be near the lower limit of detection, such that (hypothetically) stochasticity in the qPCR process shouldn't be ignored. See:
If you're interested by this work, feel free to get in touch with me, or take a look at what SecureBio have been doing more recently!
Owner
- Name: Adam Howes
- Login: athowes
- Kind: user
- Location: London, UK
- Company: Imperial College London
- Website: athowes.github.io
- Twitter: adamhowes
- Repositories: 8
- Profile: https://github.com/athowes
Citation (citations.bib)
@article{consortium2021global,
title={A Global Nucleic Acid Observatory for Biodefense and Planetary Health},
author={{The Nucleic Acid Observatory Consortium}},
journal={arXiv preprint arXiv:2108.02678},
year={2021}
}
GitHub Events
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Last Year
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Last synced: 10 months ago
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- Total issues: 14
- Total pull requests: 0
- Average time to close issues: 8 months
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- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.71
- 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
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Top Authors
Issue Authors
- athowes (13)