{"id":24132861,"url":"https://github.com/rrrlw/mir_combo_targeting","last_synced_at":"2026-01-25T08:31:49.658Z","repository":{"id":94234371,"uuid":"300452454","full_name":"rrrlw/MiR_Combo_Targeting","owner":"rrrlw","description":"Companion code for the paper: \"Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma\"","archived":false,"fork":false,"pushed_at":"2020-09-22T01:35:33.000Z","size":18437,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-06-03T02:56:26.573Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":false,"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/rrrlw.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-10-01T23:39:45.000Z","updated_at":"2021-09-09T18:00:25.000Z","dependencies_parsed_at":null,"dependency_job_id":"d15cf3a5-cd68-4892-b69a-e9dc4aa1d488","html_url":"https://github.com/rrrlw/MiR_Combo_Targeting","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/rrrlw/MiR_Combo_Targeting","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rrrlw%2FMiR_Combo_Targeting","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rrrlw%2FMiR_Combo_Targeting/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rrrlw%2FMiR_Combo_Targeting/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rrrlw%2FMiR_Combo_Targeting/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rrrlw","download_url":"https://codeload.github.com/rrrlw/MiR_Combo_Targeting/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rrrlw%2FMiR_Combo_Targeting/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28749326,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-25T08:31:04.260Z","status":"ssl_error","status_checked_at":"2026-01-25T08:30:28.859Z","response_time":113,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":"2025-01-11T22:38:43.657Z","updated_at":"2026-01-25T08:31:49.646Z","avatar_url":"https://github.com/rrrlw.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# MiR_Combo_Targeting\nCompanion code for the paper: \"Network potential identifies therapeutic miRNA cocktails in Ewing sarcoma\"\nYou can find the pre-print for this analysis here.https://www.biorxiv.org/content/10.1101/854695v1\nIf you have any questions regarding how to run this pipeline on your device/ use it for your research, \nfeel free to shoot me an email at davis.weaver@case.edu. \n\n## Here is the general flow: \n1. Main_EWS_miR (by calling the functions in NP_pipeline_MiR and NP_Funcs_MiR) converts the processed RNA sequencing data and the biogrid PPI into cell signaling networks and does in-silico repression experiments to generate a list of protein targets. This step made use of ~20 cores of an HPC. Attempting to do it on a laptop or desktop would likely take a period of days to weeks. \n2. miR_Analysis_Ewing (by calling the functions in miR_Analysis_Functions) processes the results of Main_EWS_miR and evaluates miR cocktails to identify optimal 3 miR combinations. \n3. miR_Figs_Ewing produces all the figures and tables from the paper using the output of both miR_Analysis_Ewing and Main_EWS_miR.\n\n## Dependencies:\nPackage dependencies are at the top of each script. \nEach script also requires data files to run. \n\n1. Main_EWS_miR.R\n    * rld_counts.csv\n    * BIOGRID-ORGANISM-Homo_sapiens-3.5.171.tab2.txt\n2. miR_Analysis_Ewing.R\n    * EwingsDatasetFinal.csv\n    * all_miRNA_targets.rda\n    * Census_allMon_2019.csv\n    * Housekeeping_GenesHuman.csv\n3. miR_Figs_Ewing\n    * Protein_RNA_correlation.csv\n \nCreate a folder in the folder where you store the code called \"data_files\". Download these 7 dependencies do that folder and then it should (hopefully) all go. \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frrrlw%2Fmir_combo_targeting","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frrrlw%2Fmir_combo_targeting","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frrrlw%2Fmir_combo_targeting/lists"}