https://github.com/alserglab/coresh
Science Score: 26.0%
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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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○Scientific vocabulary similarity
Low similarity (4.0%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: alserglab
- License: other
- Default Branch: main
- Size: 3.91 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
This repository demonstrates the core algorithm behind CORESH search engine for querying public gene expression datasets based on a user-provided gene signature (https://alserglab.wustl.edu/coresh/).
CORESH ranks the datasets based on the level of coregulation of user-provided genes using a score inspired by Principal Component Analysis, which can be applied to any gene expression matrix. Currently, CORESH operates on a compendium of more than 40,000 mouse and 40,000 human gene expression datasets from the GEO database, including datasets from both microarray and RNA-seq profiling.
Please refer to the vignette at https://rpubs.com/asergushichev/coresh-local.
Owner
- Name: alserglab
- Login: alserglab
- Kind: organization
- Repositories: 1
- Profile: https://github.com/alserglab
GitHub Events
Total
- Release event: 1
- Push event: 2
- Create event: 3
Last Year
- Release event: 1
- Push event: 2
- Create event: 3
Dependencies
- BiocParallel * imports
- data.table * imports
- dplyr * imports
- fastmatch * imports
- fgsea * imports
- msigdbr >= 10 imports
- qs2 * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests