{"id":17030589,"url":"https://github.com/vsoch/gene2drug","last_synced_at":"2025-03-22T20:28:09.400Z","repository":{"id":20958070,"uuid":"24246741","full_name":"vsoch/gene2drug","owner":"vsoch","description":"A toolbox to find if gene sets and drugs are meaningfully related [in development]","archived":false,"fork":false,"pushed_at":"2014-09-22T21:52:53.000Z","size":19200,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-28T00:29:52.872Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/vsoch.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-09-19T21:56:18.000Z","updated_at":"2022-07-17T08:43:42.000Z","dependencies_parsed_at":"2022-07-23T15:32:16.501Z","dependency_job_id":null,"html_url":"https://github.com/vsoch/gene2drug","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fgene2drug","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fgene2drug/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fgene2drug/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vsoch%2Fgene2drug/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vsoch","download_url":"https://codeload.github.com/vsoch/gene2drug/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245017899,"owners_count":20547894,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-14T08:07:35.234Z","updated_at":"2025-03-22T20:28:09.380Z","avatar_url":"https://github.com/vsoch.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# gene2drug\n\nUNDER DEVELOPMENT\n\nThis 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:\n\n## Gene Set Enrichment Analysis\n1) Perform GSEA (gene set enrichment analysis) to test gene sets against a database of thousands of drug compounds\n  \n###GSEA/\n- cmapGSEA.R: convert expression objects (.bz2 files) to expression matrices\n- cmapGSEARMA.R: runs gene set enrichment analysis with quantile normalization of above\n- findSigResultsDrug.R: parses GSEA results and returns significant genes, drugs, etc. for a specified FDR threshold\n- parseDrugResult.R: format results into object that includes:\n  - *geneLists*: a list of core enriched genes for each drug\n  - *meds*: a list of drugs with significantly enriched genes\n  - *report*: The full report table from GSEA\n  - *genematrix*: a binary matrix of drugs by genes, with 1 indicated significant enrichment\n  - *tanimotos*: tanimoto scores to assess similarity of drugs based on enriched genes\n  - *terms*: gene set names that are significantly enriched for each drug\n\n## PubChem\n2) Extract structure and properties of drugs from Pubchem\n- downloadPubChem.R: create table of drug properties, and download structure and bioassay json files\n\n## gene2drug Enrichment Scoring\n3) \n\n### TODO:\n- map genes to proteins\n- calculate enrichment score of proteins in my drugs\n- generate final report\n\n## Visualize \u0026 Summarize Results\n\n### gephi/\n- export data for gephi (not useful!)\n- exportd3: todo: will export drug to visualize in d3\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvsoch%2Fgene2drug","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvsoch%2Fgene2drug","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvsoch%2Fgene2drug/lists"}