{"id":23646945,"url":"https://github.com/exitare/vae-subtype-sample-generation","last_synced_at":"2026-07-16T03:32:10.024Z","repository":{"id":50387448,"uuid":"518919987","full_name":"Exitare/VAE-Subtype-Sample-Generation","owner":"Exitare","description":null,"archived":false,"fork":false,"pushed_at":"2022-10-12T03:28:52.000Z","size":2629,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-20T03:41:49.399Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/Exitare.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":"2022-07-28T16:32:21.000Z","updated_at":"2022-08-11T16:28:28.000Z","dependencies_parsed_at":"2023-01-19T21:46:07.955Z","dependency_job_id":null,"html_url":"https://github.com/Exitare/VAE-Subtype-Sample-Generation","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Exitare/VAE-Subtype-Sample-Generation","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exitare%2FVAE-Subtype-Sample-Generation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exitare%2FVAE-Subtype-Sample-Generation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exitare%2FVAE-Subtype-Sample-Generation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exitare%2FVAE-Subtype-Sample-Generation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Exitare","download_url":"https://codeload.github.com/Exitare/VAE-Subtype-Sample-Generation/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Exitare%2FVAE-Subtype-Sample-Generation/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35529628,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-16T02:00:06.687Z","response_time":83,"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":[],"created_at":"2024-12-28T13:48:10.158Z","updated_at":"2026-07-16T03:32:10.002Z","avatar_url":"https://github.com/Exitare.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# VAE-Subtype-Sample-Generation operations\n### Goal: Generate TCGA cohort samples\n    based on encoding of all TCGA samples\n    use gene expression data type only\n\npip install -r requirements.txt  \npython3 -m venv venv  \nsource venv/bin/activate  \n\n### 2022-10-04  \nVAE_smpl_gen_04.ipynb pushed, connected to UMAP now  \n\n2022-08-08\ntest on 1000 x 100 make_classification fabricated data\nUse latent space dimension of 10 b/c order mag \u003c 100\nsbatch fbrctd.sh 10 fbrctd_00 data/1000_100_X.tsv\n\n2022-08-03\nfile prepped with 8009 samples and 99 subtypes\nlabels encoded\nto /VAE-Subtype-Sample-Generation/data on Exacloud\nsbatch sample_gen_data.sh 1000 v0.2 data/cmbnd_25_lbl_xfrm.tsv\n* expecting out_of_memory fail\n\n2022-08-02\nsbatch sample_gen.sh -lt 1000 -p v00 --data data/BRCA_feat_ntrsct_25.tsv\nsbatch sample_gen.sh 1000 v0.1 path_to_file\nsbatch sample_gen_data.sh 1000 v0.1 data/BRCA_feat_ntrsct_25.tsv\n\nnext actions:\n    clone into Exacloud\n    upload gene expression extraction from molecular file scripts\n    read direct from GDAN TMP dir (?)\n\n2022-07-28\n\noutput and error report directories setup\n\n25 is latent space column dimension\nv03 is result dir name\nsbatch sample_gen.sh 25 v03 data/trn_v00.tsv data/val_v00.tsv data/tst_v00.tsv\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fexitare%2Fvae-subtype-sample-generation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fexitare%2Fvae-subtype-sample-generation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fexitare%2Fvae-subtype-sample-generation/lists"}