{"id":20074739,"url":"https://github.com/greenelab/adage","last_synced_at":"2026-03-07T00:33:14.900Z","repository":{"id":79358894,"uuid":"45477517","full_name":"greenelab/adage","owner":"greenelab","description":"Data and code related to the paper \"ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa...\" Jie Tan, et al · mSystems · 2016","archived":false,"fork":false,"pushed_at":"2016-05-26T02:15:39.000Z","size":82958,"stargazers_count":61,"open_issues_count":0,"forks_count":30,"subscribers_count":13,"default_branch":"master","last_synced_at":"2025-10-09T11:12:24.829Z","etag":null,"topics":["autoencoders","data","dataset","denoising-autoencoders","gene-expression","machine-learning","manuscript","methodology","neural-networks","paper","pseudomonas-aeruginosa","research","supplement"],"latest_commit_sha":null,"homepage":"","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/greenelab.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}},"created_at":"2015-11-03T15:56:31.000Z","updated_at":"2024-12-07T13:31:52.000Z","dependencies_parsed_at":"2023-04-16T14:33:26.488Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/adage","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/greenelab/adage","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fadage","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fadage/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fadage/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fadage/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/adage/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fadage/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30204154,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-06T19:07:06.838Z","status":"ssl_error","status_checked_at":"2026-03-06T18:57:34.882Z","response_time":250,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":["autoencoders","data","dataset","denoising-autoencoders","gene-expression","machine-learning","manuscript","methodology","neural-networks","paper","pseudomonas-aeruginosa","research","supplement"],"created_at":"2024-11-13T14:54:07.192Z","updated_at":"2026-03-07T00:33:09.862Z","avatar_url":"https://github.com/greenelab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# adage\n[![DOI](https://zenodo.org/badge/19060/greenelab/adage.svg)](https://zenodo.org/badge/latestdoi/19060/greenelab/adage)\n\nThis is the repository for ADAGE (Analysis using Denoising Autoencoders for Gene Expression)\n\nThis repository provides the source code in support of the manuscript: [ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions](http://msystems.asm.org/content/1/1/e00025-15). J Tan, JH Hammond, DA Hogan, CS Greene. *mSystems*, 00025-15. \n\n############################################################\n\nTo set up ADAGE, first clone the repository. This is a short summary. Detailed instructions and steps to generate the model and reproduce analyses used in the manuscript are in pseudomonas_autoencoder.sh \n\nBuilding an ADAGE model requires installing python packages Theano and Docopt \nInstructions for Theano: http://deeplearning.net/software/theano/install.html \nInstructions for docopt: https://pypi.python.org/pypi/docopt\n\nWe provide a gene expression compendium of Pseudomonas aeruginosa that contains datasets available before 02.22.2014. To get an up-to-date compendium, follow the instructions in Section One in pseudomonas_autoencoder.sh \n\nBefore training, first 0-1 normalize the compendium, run\npython Data_collection_processing/zero_one_normalization.py Data_collection_processing/Pa_compendium_02.22.2014.pcl Train_test_DAs/train_set_normalized.pcl None\n\nTo train a denoising autoencoders, run \npython Train_test_DAs/SdA_train.py Train_test_DAs/train_set_normalized.pcl --parameters\n\nTo test a dataset on an ADAGE model, run\npython Train_test_DAs/SdA_test.py Train_test_DAs/Genome-hybs_normalized.pcl --parameters\n \n############################################################\n\nPlease email jie.tan.gr@dartmouth.edu if you have questions.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fadage","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fadage","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fadage/lists"}