{"id":17961274,"url":"https://github.com/erictleung/bmi656-research-project","last_synced_at":"2025-10-07T15:40:34.980Z","repository":{"id":72464094,"uuid":"26929950","full_name":"erictleung/bmi656-research-project","owner":"erictleung","description":"Final project for BMI 656 Bioinformatics Programming and Scripting","archived":false,"fork":false,"pushed_at":"2018-12-06T02:20:30.000Z","size":783,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-08-18T05:49:56.963Z","etag":null,"topics":["class-project","h5n1","kegg-pathways","odds-ratio","project","python","python-programming"],"latest_commit_sha":null,"homepage":"","language":"Python","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/erictleung.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":"2014-11-20T20:14:15.000Z","updated_at":"2018-12-06T01:31:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"73719cca-970d-4e4d-94d9-19428615a1f1","html_url":"https://github.com/erictleung/bmi656-research-project","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/erictleung/bmi656-research-project","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fbmi656-research-project","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fbmi656-research-project/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fbmi656-research-project/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fbmi656-research-project/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/erictleung","download_url":"https://codeload.github.com/erictleung/bmi656-research-project/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/erictleung%2Fbmi656-research-project/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278801800,"owners_count":26048557,"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","status":"online","status_checked_at":"2025-10-07T02:00:06.786Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["class-project","h5n1","kegg-pathways","odds-ratio","project","python","python-programming"],"created_at":"2024-10-29T11:08:50.347Z","updated_at":"2025-10-07T15:40:34.960Z","avatar_url":"https://github.com/erictleung.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"bmi656-research-project\n=======================\n\nThis repository contains the files for the final project in BMI 656.\n\n# odds.py\n\nThis script will perform an odds ratio calculation to identify pathways\ncontaining a larger number of differentially expressed genes than would be\nexpected by chance.\n\nThis script will assume you have the following text files in the current\ndirectory:\n\n+ H5N1_VN1203_DE_Probes.txt\n+ H5N1_VN1203_UNIVERSE_Probes.txt\n+ KEGG_Pathway_Genes.txt\n\nThe script will parse through each of them and find KEGG pathways which have an\nodds ratio greater than 1.5. A KEGG pathway will be chose out of the ones with\nan odds ratio greater than 1.5 to study further in the next section.\n\n# crossSpecies.py\n\n# Deliverables \n\n+ (60 points) Write Part I and Part II as separate python programs that are both called from a linux bash script. This script should check for the existence of relevant files and check that Part I has successfully completed before running Part II. Turn in both python programs and the bash script. \n+ (10 points) Screen shot of pathway with highlighted differentially expressed genes \n+ (10 points) Boxplot labeled with p-value of **Mann-Whitney statistic** \n+ (20 points) 1-2 page write-up summarizing your findings. This should be a word document that includes at least 2\nfigures corresponding to your pathway and boxplot. Discuss the limitations of the study and any obstacles/problems you experienced. Discuss the relevance of the pathway to H5N1 infection. Discuss why the conservation of the affected pathway might be important for the study of H5N1 (Hint: think about our use of model organisms to study infectious diseases). \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ferictleung%2Fbmi656-research-project","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ferictleung%2Fbmi656-research-project","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ferictleung%2Fbmi656-research-project/lists"}