{"id":20074709,"url":"https://github.com/greenelab/multiple-myeloma-classifier","last_synced_at":"2026-02-05T16:31:53.169Z","repository":{"id":79359647,"uuid":"131507207","full_name":"greenelab/multiple-myeloma-classifier","owner":"greenelab","description":"Multi-class KRAS/NRAS Classifier for Multiple Myeloma","archived":false,"fork":false,"pushed_at":"2019-03-07T14:50:51.000Z","size":1598,"stargazers_count":4,"open_issues_count":2,"forks_count":4,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-07-08T18:10:27.351Z","etag":null,"topics":["analysis","cancer","dataset","gene-expression","machine-learning","methodology"],"latest_commit_sha":null,"homepage":"","language":"HTML","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/greenelab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","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":"2018-04-29T15:41:19.000Z","updated_at":"2024-03-12T12:43:13.000Z","dependencies_parsed_at":"2023-03-09T04:15:31.906Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/multiple-myeloma-classifier","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/greenelab/multiple-myeloma-classifier","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fmultiple-myeloma-classifier","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fmultiple-myeloma-classifier/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fmultiple-myeloma-classifier/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fmultiple-myeloma-classifier/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/multiple-myeloma-classifier/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fmultiple-myeloma-classifier/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29125837,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-05T14:05:12.718Z","status":"ssl_error","status_checked_at":"2026-02-05T14:03:53.078Z","response_time":65,"last_error":"SSL_read: 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":["analysis","cancer","dataset","gene-expression","machine-learning","methodology"],"created_at":"2024-11-13T14:53:51.095Z","updated_at":"2026-02-05T16:31:53.152Z","avatar_url":"https://github.com/greenelab.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Training and Evaluating a Multiclass Classifier for Multiple Myeloma\n\n**Gregory Way and Casey Greene 2018**\n\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2566059.svg)](https://doi.org/10.5281/zenodo.2566059)\n\nIn the following analysis, we train a multiclass classifier on RNAseq data of patients with Multiple Myeloma.\nThe classifier is trained to distinguish _KRAS_ and _NRAS_ mutations from wild-type tumors.\n\nThe analysis is presented in the following preprint:\n\n\u003e Yu-Hsiu Tony Lin,  Gregory P. Way,  Benjamin G. Barwick, Margarette C. Mariano, Makeba Marcoulis, Ian D. Ferguson, Christoph Driessen, Lawrence H. Boise, Casey S. Greene, Arun P. Wiita.\n\u003e _Integrated Phosphoproteomics and Transcriptional Classifiers Reveal Hidden RAS Signaling Dynamics in Multiple Myeloma_.\n\u003e February 29th, 2019. _biorXiv_ https://doi.org/10.1101/563312.\n\n## Data\n\nThe data was provided by Arun Wiita and Tony Lin (UCSF) as part of the [MMRF CoMMpass Study](https://www.themmrf.org/research-partners/mmrf-data-bank/the-mmrf-commpass-study/).\nThe data was accessed in a Box link provided by Arun and Tony. Before performing the analysis, the appropriate data must be deposited into the appropriate folders.\nThe data are not included in this repository.\n\nThe analysis expects the following data in the `data/raw/` folder:\n\n1. CoMMpass_train_set.csv \n2. CoMMpass_train_set_labels.csv\n3. CoMMpass_test_set.csv\n4. CoMMpass_test_set_labels.csv\n5. MMCL_RNAseq.csv\n6. MMCL_RNAseq_labels.csv\n7. gprofiler_results_1002952837509.xlsx\n\nIf the data are not deposited in the `data/raw` folder, the analysis will not run.\nWe will provide a reproducible solution by depositing data in an archived and versioned database at a later date.\n\n## Computational Environment\n\nWe use conda (`version 4.5.2`) to manage our computational environment.\nAll scripts must be run in this environment.\nAfter [installing conda](https://conda.io/docs/user-guide/install/index.html), run the following:\n\n```bash\n# Initialize the environment\nconda env create --force --file environment.yml\n\n# Activate the environment\nconda activate multiple-myeloma-classifier\n```\n\n## Analysis Pipeline\n\nThe analysis consists of a series of notebooks that are designed to be run in order.\nSee `run_analysis.sh` for more details.\n\nNotebooks are converted into python `.py` files and stored in the `scipts/` folder with:\n\n```bash\njupyter nbconvert --to=script --FilesWriter.build_directory=scripts *.ipynb\n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fmultiple-myeloma-classifier","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fmultiple-myeloma-classifier","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fmultiple-myeloma-classifier/lists"}