{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"scrumlord","owner":"greenelab","isFork":false,"description":"Continuous administration of the Greene Lab's electronic scrum","allTopics":["administration","cron","travis-ci","scrum","continuous"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":13,"forksCount":8,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-07T22:41:43.662Z"}},{"type":"Public","name":"adage-backend","owner":"greenelab","isFork":false,"description":"The backend for Adage web app","allTopics":["machine-learning","web-server","genomics","interpretation"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":9,"starsCount":2,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-21T08:32:33.794Z"}},{"type":"Public","name":"buddi","owner":"greenelab","isFork":false,"description":"BuDDI model implementation","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-10T20:49:29.643Z"}},{"type":"Public","name":"pubtator","owner":"greenelab","isFork":false,"description":"Retrieve and process PubTator annotations","allTopics":["nlp","data","text-mining","tool","pubmed","snorkel","pubtator"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":5,"starsCount":40,"forksCount":9,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-10T14:33:37.199Z"}},{"type":"Public","name":"preprint-similarity-search","owner":"greenelab","isFork":false,"description":"A web app that uses machine learning to recommend the most suitable journals based on the text content of your preprint","allTopics":["nlp","web-app","journals","nlp-machine-learning"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":22,"issueCount":4,"starsCount":19,"forksCount":4,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-23T01:19:29.482Z"}},{"type":"Public","name":"connectivity-search-backend","owner":"greenelab","isFork":false,"description":"Django backend for hetnet connectivity search","allTopics":["django","backend","hetio","hetmech","hetnets","hetnet-connectivity-search","database"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":6,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-30T14:58:17.684Z"}},{"type":"Public","name":"tribe","owner":"greenelab","isFork":false,"description":"An open-source webserver that allows for easy, reproducible genomics analyses between different webservers","allTopics":["gene-sets","web-server","server","tool"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":11,"issueCount":12,"starsCount":3,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-08T01:39:22.738Z"}},{"type":"Public","name":"indices_app","owner":"greenelab","isFork":false,"description":"The code for the web app for https://github.com/greenelab/indices","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-28T15:50:23.019Z"}},{"type":"Public","name":"wenda_gpu","owner":"greenelab","isFork":false,"description":"Fast domain adaptation method for building prediction models on genomic data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-18T19:04:11.923Z"}},{"type":"Public","name":"wenda_gpu_paper","owner":"greenelab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-29T20:48:13.795Z"}},{"type":"Public","name":"ponyo","owner":"greenelab","isFork":false,"description":"Software to simulate compendium-wide gene expression data using a VAE.","allTopics":["machine-learning","neural-network","gene-expression","software","autoencoder","data-simulation","variational-autoencoder"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":4,"starsCount":1,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-28T18:18:50.117Z"}},{"type":"Public","name":"word-lapse-models","owner":"greenelab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-05-20T22:15:28.054Z"}},{"type":"Public","name":"disease_ontology_geneset","owner":"greenelab","isFork":false,"description":"","allTopics":["database","geneset"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-01T11:13:03.160Z"}},{"type":"Public","name":"cimr","owner":"greenelab","isFork":false,"description":"tool for continuously integrated meta-resource","allTopics":["gwas","continuous-integration","gene-expression","gtex","twas"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":2,"starsCount":1,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-03-25T22:46:31.974Z"}},{"type":"Public","name":"kegg_geneset","owner":"greenelab","isFork":false,"description":"Biothings data plugin for KEGG genesets","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-01-21T23:55:26.532Z"}},{"type":"Public","name":"wiki-nationality-estimate","owner":"greenelab","isFork":false,"description":"Name-based nationality prediction trained on Wikipedia","allTopics":["machine-learning","wikipedia","nationalize"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":2,"starsCount":4,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-10-29T15:19:37.726Z"}},{"type":"Public","name":"shared-latent-space","owner":"greenelab","isFork":false,"description":"Shared Latent Space VAE's","allTopics":["machine-learning","analysis","autoencoder","methodology","variational-autoencoder"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":16,"starsCount":21,"forksCount":5,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-04-20T15:40:06.556Z"}},{"type":"Public","name":"tad_pathways_pipeline","owner":"greenelab","isFork":false,"description":"Pipeline to implement a \"TAD_Pathways\" analysis. Discover candidate genes based on association signals in TADs","allTopics":["workflow","candidate-genes","tad","methodology","pathways","tads","gwas","analysis"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":4,"starsCount":11,"forksCount":5,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-12-21T15:21:58.286Z"}},{"type":"Public","name":"django-genes","owner":"greenelab","isFork":false,"description":"A Django package to represent genes","allTopics":["web-server","server","tool"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":12,"starsCount":2,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-02-14T15:09:59.554Z"}},{"type":"Public","name":"django-organisms","owner":"greenelab","isFork":false,"description":"A Django package to represent organisms","allTopics":["web-server","server","tool"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-02-11T21:00:19.820Z"}},{"type":"Public","name":"GEA_Community_Detection","owner":"greenelab","isFork":false,"description":"Overrepresentation analysis for KEGG and PID pathways using community detection","allTopics":["analysis","pid","gene-expression","networks","pathway-analysis","kegg-pathway","pathway","detection-network","enrichment-analysis"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":7,"forksCount":6,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-01-07T00:47:34.360Z"}},{"type":"Public","name":"annotation-refinery","owner":"greenelab","isFork":false,"description":"A python package that consists of functions that process publicly available annotated sets of genes","allTopics":["package","gene-sets","script","tool","ontology"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":6,"starsCount":5,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-12-18T20:45:36.326Z"}},{"type":"Public","name":"tribe-client","owner":"greenelab","isFork":false,"description":"A client for an open-source web app that allows creating, sharing, and analyzing gene sets","allTopics":["gene-sets","tool"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":0,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-11-02T20:54:05.570Z"}},{"type":"Public","name":"PathCORE-T","owner":"greenelab","isFork":false,"description":"Methods to build a network of pathway co-occurrence relationships out of expression signatures extracted from transcriptomic compendia.","allTopics":["analysis","gene-expression","methodology","supplement"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":4,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-17T15:51:12.137Z"}},{"type":"Public","name":"bioconductor-scraper","owner":"greenelab","isFork":false,"description":"A scraper which tries to generate conda recipes for bioconductor and other needed R packages.","allTopics":["script","tool","scraper","bioconductor"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-06-05T17:50:39.556Z"}},{"type":"Public","name":"tad_pathways","owner":"greenelab","isFork":false,"description":"DEPRECATED: Integrating topologically associating domains (TADs) to prioritize GWAS signal","allTopics":["analysis","deprecated","methodology","pathway"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":1,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-04-21T17:37:07.031Z"}},{"type":"Public","name":"nf1_inactivation","owner":"greenelab","isFork":false,"description":"Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation","allTopics":["machine-learning","analysis","cancer","gene-expression","methodology"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":11,"forksCount":6,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-12-19T13:47:27.537Z"}},{"type":"Public","name":"staNMF","owner":"greenelab","isFork":false,"description":"A python implementation of Stability NMF","allTopics":["machine-learning","analysis","tool","gene-expression"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":6,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-11-23T18:58:18.580Z"}},{"type":"Public","name":"adage","owner":"greenelab","isFork":false,"description":"Data and code related to the paper \"ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa...\" Jie Tan, et al · mSystems · 2016","allTopics":["data","machine-learning","research","paper","dataset","neural-networks","methodology","manuscript","autoencoders","supplement","gene-expression","denoising-autoencoders","pseudomonas-aeruginosa"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":63,"forksCount":30,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-05-26T02:15:39.655Z"}},{"type":"Public","name":"gcb535challenge","owner":"greenelab","isFork":false,"description":"We play a prediction game in our GCB 535 class. The class aims to teach students, primarily biologists, about machine learning methods and their use. This repository hosts the challenge for individuals outside of our lab.","allTopics":["biology","class","exercise","teaching","challenge","dataset"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":8,"forksCount":4,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-04-08T13:46:58.270Z"}}],"repositoryCount":31,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}