{"id":26216057,"url":"https://github.com/borgwardtlab/human_scdvp_analysis","last_synced_at":"2025-06-29T06:06:28.726Z","repository":{"id":279231174,"uuid":"938123127","full_name":"BorgwardtLab/Human_scDVP_Analysis","owner":"BorgwardtLab","description":null,"archived":false,"fork":false,"pushed_at":"2025-03-26T14:32:19.000Z","size":33061,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-26T14:43:12.900Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BorgwardtLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2025-02-24T13:08:57.000Z","updated_at":"2025-03-26T14:32:23.000Z","dependencies_parsed_at":"2025-02-24T14:46:47.790Z","dependency_job_id":null,"html_url":"https://github.com/BorgwardtLab/Human_scDVP_Analysis","commit_stats":null,"previous_names":["borgwardtlab/human_scdvp_analysis"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BorgwardtLab/Human_scDVP_Analysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FHuman_scDVP_Analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FHuman_scDVP_Analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FHuman_scDVP_Analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FHuman_scDVP_Analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BorgwardtLab","download_url":"https://codeload.github.com/BorgwardtLab/Human_scDVP_Analysis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FHuman_scDVP_Analysis/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262545031,"owners_count":23326658,"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":"2025-03-12T11:19:18.755Z","updated_at":"2025-06-29T06:06:28.551Z","avatar_url":"https://github.com/BorgwardtLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Human scDVP data analysis\n\nData analysis scripts for \"Spatial single-cell proteomics enables continuous mapping of protein gradients in human liver tissues\".\n\n### Installation\n\nTo install the software, first create an isolated conda environment, and add [poetry](https://python-poetry.org/) (our dependency manager of choice) to its dependencies:\n\n```bash\nconda create -n humanscDVP python=3.11 poetry\nconda activate humanscDVP\n```\n\nNavigate to the repository folder, and run:\n\n```bash\npoetry install\n```\n\nIn order to convert mouse gene names to their human orthologs, you will also need to install the [pyorthomap](https://github.com/vitkl/orthologsBioMART) package from GitHub:\n\n```bash\npip install git+https://github.com/vitkl/orthologsBioMART.git\n```\n\n### Usage\n\nTo reproduce the output provided in `results`, run the following sequence of commands:\n\n1. Run LMM analysis for control human samples:\n\n```bash\npython LMM_analysis.py --data_path ../data/human/ --patient_group 1 --plot --save --species human\n```\n\n2. Run LMM analysis for fibrotic human samples:\n\n```bash\npython LMM_analysis.py --data_path ../data/human/ --patient_group 2 --plot --save --species human\n```\n\n3. Run LMM analysis for mouse samples:\n\n```bash\npython LMM_analysis.py --data_path ../data/mouse/ --patient_group 3 --plot --save --species mouse\n```\n\n4. Compare slopes between control and fibrotic human samples:\n\n```bash\npython Compare_slopes.py --control_model_results ../results/human_controls/results_1_cutoff\\=0.7.tsv --treatment_model_results ../results/human_fibrotic/results_2_cutoff\\=0.7.tsv --plot --one_sided\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fhuman_scdvp_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fborgwardtlab%2Fhuman_scdvp_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fhuman_scdvp_analysis/lists"}