https://github.com/vsoch/gene2drug
A toolbox to find if gene sets and drugs are meaningfully related [in development]
https://github.com/vsoch/gene2drug
Last synced: over 1 year ago
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A toolbox to find if gene sets and drugs are meaningfully related [in development]
- Host: GitHub
- URL: https://github.com/vsoch/gene2drug
- Owner: vsoch
- Created: 2014-09-19T21:56:18.000Z (almost 12 years ago)
- Default Branch: master
- Last Pushed: 2014-09-22T21:52:53.000Z (almost 12 years ago)
- Last Synced: 2025-01-28T00:29:52.872Z (over 1 year ago)
- Language: R
- Size: 18.3 MB
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# gene2drug
UNDER DEVELOPMENT
This toolbox will take a set of genes, and allow a researcher to determine if any of the genes are meaningfully related to drugs. The algorithm works as follows:
## Gene Set Enrichment Analysis
1) Perform GSEA (gene set enrichment analysis) to test gene sets against a database of thousands of drug compounds
###GSEA/
- cmapGSEA.R: convert expression objects (.bz2 files) to expression matrices
- cmapGSEARMA.R: runs gene set enrichment analysis with quantile normalization of above
- findSigResultsDrug.R: parses GSEA results and returns significant genes, drugs, etc. for a specified FDR threshold
- parseDrugResult.R: format results into object that includes:
- *geneLists*: a list of core enriched genes for each drug
- *meds*: a list of drugs with significantly enriched genes
- *report*: The full report table from GSEA
- *genematrix*: a binary matrix of drugs by genes, with 1 indicated significant enrichment
- *tanimotos*: tanimoto scores to assess similarity of drugs based on enriched genes
- *terms*: gene set names that are significantly enriched for each drug
## PubChem
2) Extract structure and properties of drugs from Pubchem
- downloadPubChem.R: create table of drug properties, and download structure and bioassay json files
## gene2drug Enrichment Scoring
3)
### TODO:
- map genes to proteins
- calculate enrichment score of proteins in my drugs
- generate final report
## Visualize & Summarize Results
### gephi/
- export data for gephi (not useful!)
- exportd3: todo: will export drug to visualize in d3