{"payload":{"pageCount":42,"repositories":[{"type":"Public","name":"ABC-Enhancer-Gene-Prediction","owner":"broadinstitute","isFork":false,"description":"Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":11,"starsCount":188,"forksCount":55,"license":"MIT License","participation":[10,10,0,15,2,2,1,2,4,6,7,3,3,2,0,0,0,3,0,0,0,6,3,4,3,4,14,20,4,3,0,0,0,1,2,2,1,7,3,10,11,0,6,2,0,0,2,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T22:09:19.406Z"}},{"type":"Public","name":"long-read-pipelines","owner":"broadinstitute","isFork":false,"description":"Long read production pipelines","allTopics":["pipelines","wdl","variant-calling","de-novo-assembly","long-reads"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":16,"issueCount":95,"starsCount":121,"forksCount":23,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,0,0,0,0,0,2,2,0,0,2,0,0,0,0,0,0,0,1,2,0,2,0,0,0,0,0,2,0,0,0,0,2,0,0,0,0,0,2,0,0,0,0,2,0,0,2,2,2,2,2,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T22:02:55.523Z"}},{"type":"Public","name":"syma","owner":"broadinstitute","isFork":false,"description":"Symbolic math","allTopics":[],"primaryLanguage":{"name":"Rust","color":"#dea584"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,4],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:55:11.120Z"}},{"type":"Public","name":"jati","owner":"broadinstitute","isFork":false,"description":"DSL support library based on nom.","allTopics":[],"primaryLanguage":{"name":"Rust","color":"#dea584"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[2,1,0,0,0,0,0,0,0,3,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:54:33.006Z"}},{"type":"Public","name":"2022_PERISCOPE","owner":"broadinstitute","isFork":false,"description":"This repository contains all supporting analyses and files for Ramezani, Bauman, Singh, and Weisbart, et al. \"A genome-wide atlas of human cell morphology\". ","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":3,"starsCount":2,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,0,2,1,1,11,3,0,1,1,2,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,7,1,5,7,1,3,9,3,0,0,0,9],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:46:49.142Z"}},{"type":"Public","name":"cromwhelm","owner":"broadinstitute","isFork":false,"description":"Tentative first steps into the world of helm charts","allTopics":[],"primaryLanguage":{"name":"Smarty","color":"#f0c040"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":2,"license":null,"participation":[29,23,13,14,5,19,2,6,26,6,23,24,8,8,11,6,14,14,10,14,4,4,10,6,8,2,16,18,10,0,0,12,2,8,2,12,8,12,14,10,12,12,8,10,10,10,0,2,10,10,14,2],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:36:57.185Z"}},{"type":"Public","name":"cromwell","owner":"broadinstitute","isFork":false,"description":"Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments","allTopics":["docker","application","cloud","bioinformatics","scala","executor","hpc","containers","wdl","ga4gh","workflow-description-language","workflow-execution","workflow"],"primaryLanguage":{"name":"Scala","color":"#c22d40"},"pullRequestCount":39,"issueCount":727,"starsCount":963,"forksCount":351,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[4,2,1,2,1,2,2,3,4,1,5,6,1,0,0,2,2,4,4,3,0,1,4,2,1,0,6,8,5,0,0,4,1,2,1,3,1,3,6,3,4,5,0,2,5,5,0,1,8,7,8,2],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:29:54.418Z"}},{"type":"Public","name":"gnomad-browser","owner":"broadinstitute","isFork":false,"description":"Explore gnomAD datasets on the web","allTopics":["javascript","genomics","gnomad"],"primaryLanguage":{"name":"TypeScript","color":"#3178c6"},"pullRequestCount":31,"issueCount":155,"starsCount":78,"forksCount":40,"license":"MIT License","participation":[5,5,5,6,0,4,4,0,7,2,4,4,3,2,16,17,10,8,5,10,8,85,41,16,16,6,28,7,3,1,3,6,5,9,7,6,4,3,3,6,6,2,2,8,25,12,26,15,9,5,3,8],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:28:29.991Z"}},{"type":"Public","name":"seqr","owner":"broadinstitute","isFork":false,"description":" web-based analysis tool for rare disease genomics","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":51,"starsCount":168,"forksCount":89,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:25:50.070Z"}},{"type":"Public","name":"horsefish","owner":"broadinstitute","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":15,"issueCount":0,"starsCount":5,"forksCount":7,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,1,0,0,0,0,3,0,0,1,3,1,0,0,0,1,0,2,0,1,0,0,0,0,0,0,0,1,3,1,0,0,3,0,0,1,1,8,1,5,6,1,0,1,8,0,0,0,0,1,0,4],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:16:29.089Z"}},{"type":"Public","name":"sam","owner":"broadinstitute","isFork":false,"description":"workbench identity and access management","allTopics":[],"primaryLanguage":{"name":"Scala","color":"#c22d40"},"pullRequestCount":87,"issueCount":3,"starsCount":41,"forksCount":11,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[4,4,2,3,1,2,1,2,3,1,1,1,2,0,3,1,0,3,0,6,7,7,3,7,5,6,3,10,2,0,1,2,2,1,1,4,5,5,3,2,1,1,1,2,0,1,4,3,10,3,1,6],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T21:00:49.910Z"}},{"type":"Public","name":"thelma","owner":"broadinstitute","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Go","color":"#00ADD8"},"pullRequestCount":11,"issueCount":0,"starsCount":0,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,1,0,0,0,0,0,5,1,2,4,0,0,0,1,0,11,3,1,7,2,1,0,1,1,0,7,8,0,0,0,7,2,9,2,1,2,2,0,0,0,0,0,4,2,2,0,1,1,1,1,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:53:15.172Z"}},{"type":"Public","name":"palantir-workflows","owner":"broadinstitute","isFork":false,"description":"Utility workflows for the DSP hydro.gen team (formerly palantir)","allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":4,"issueCount":6,"starsCount":18,"forksCount":6,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,2,0,0,0,1,1,1,0,2,2,0,4,2,0,2,1,1,0,0,0,0,0,3,0,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,1,2,1,1,1,0,0,0,2,2,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:47:12.017Z"}},{"type":"Public","name":"single_cell_portal_core","owner":"broadinstitute","isFork":false,"description":"Rails/Docker application for the Broad Institute's single cell RNA-seq data portal","allTopics":["rna-seq-analysis","single-cell-genomics","human-cell-atlas"],"primaryLanguage":{"name":"Ruby","color":"#701516"},"pullRequestCount":3,"issueCount":0,"starsCount":60,"forksCount":25,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[36,39,22,38,15,32,40,49,29,41,34,41,47,24,26,22,45,41,29,46,44,47,15,44,31,32,47,15,9,7,8,17,16,37,30,30,45,29,27,24,17,11,22,3,23,14,30,29,20,17,6,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:42:49.798Z"}},{"type":"Public","name":"eqtl_pipeline_terra","owner":"broadinstitute","isFork":false,"description":"scripts for eQTL pipeline in Terra","allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:40:26.793Z"}},{"type":"Public","name":"gatk-sv","owner":"broadinstitute","isFork":false,"description":"A structural variation pipeline for short-read sequencing","allTopics":["structural-variation","structural-variants","bioinformatics","genomics"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":22,"issueCount":94,"starsCount":159,"forksCount":71,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[1,2,2,5,6,1,2,1,7,6,4,3,3,2,8,2,0,0,2,2,1,0,0,0,2,0,0,1,1,0,0,4,0,3,3,2,0,0,0,3,0,0,0,0,0,1,0,10,6,6,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:29:31.630Z"}},{"type":"Public","name":"2021_09_01_VarChAMP","owner":"broadinstitute","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":8,"starsCount":0,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:29:11.732Z"}},{"type":"Public","name":"ddp-study-server","owner":"broadinstitute","isFork":false,"description":"Pepper Study Server","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":7,"issueCount":1,"starsCount":8,"forksCount":5,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[4,4,12,19,3,4,2,4,8,8,7,6,8,3,2,3,7,8,1,2,10,5,7,7,4,2,23,5,3,0,0,1,2,5,11,4,3,7,11,3,3,6,9,5,2,5,10,1,6,3,2,2],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:26:42.822Z"}},{"type":"Public","name":"seqr-loading-pipelines","owner":"broadinstitute","isFork":false,"description":"hail-based pipelines for annotating variant callsets and exporting them to elasticsearch","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":20,"starsCount":21,"forksCount":20,"license":"MIT License","participation":[57,42,49,40,42,61,43,56,65,49,21,13,39,13,59,104,10,19,2,0,0,5,11,3,8,18,15,4,1,5,2,1,2,4,5,8,28,22,43,57,29,49,6,11,5,4,6,9,4,13,3,6],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:15:30.872Z"}},{"type":"Public","name":"TerraWorkflows","owner":"broadinstitute","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":6,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,12,39,10,16,19,8,5,1,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:15:17.933Z"}},{"type":"Public","name":"juniper","owner":"broadinstitute","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":2,"issueCount":0,"starsCount":4,"forksCount":5,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[17,13,2,13,20,7,3,5,5,5,15,5,13,5,9,10,14,4,7,14,9,8,8,7,18,4,8,8,7,3,0,9,5,6,4,15,11,6,15,12,17,14,12,8,7,13,10,9,10,5,17,6],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T20:09:38.452Z"}},{"type":"Public","name":"dig-dug-portal","owner":"broadinstitute","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Vue","color":"#41b883"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[9,30,12,11,8,3,0,4,4,6,16,14,8,4,10,22,27,17,15,12,8,5,7,10,12,8,16,6,23,13,5,8,10,9,6,0,0,0,1,16,8,14,9,21,25,0,0,3,9,7,27,5],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T19:59:12.313Z"}},{"type":"Public","name":"warp","owner":"broadinstitute","isFork":false,"description":"WDL Analysis Research Pipelines","allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":24,"issueCount":7,"starsCount":190,"forksCount":88,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[14,4,12,11,1,6,10,5,1,4,6,2,4,2,2,1,4,2,2,4,4,12,3,3,9,2,5,5,5,6,0,9,3,1,3,14,13,10,14,29,4,12,11,6,6,1,0,1,0,1,5,2],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T19:51:48.034Z"}},{"type":"Public","name":"depmap_omics","owner":"broadinstitute","isFork":false,"description":"What you need to process the Quarterly DepMap-Omics releases from Terra","allTopics":["data-science","cancer-genomics","cloud-computing","depmap"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":10,"issueCount":2,"starsCount":98,"forksCount":22,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T19:42:51.351Z"}},{"type":"Public","name":"ega_submissions","owner":"broadinstitute","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,7,4,1,6,1,2,0,1,1,6,7,4,0,0,2,1,0,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T19:39:46.180Z"}},{"type":"Public","name":"gatk","owner":"broadinstitute","isFork":false,"description":"Official code repository for GATK versions 4 and up","allTopics":["science","bioinformatics","genomics","genome","ngs","sequencing","dna","spark","gatk"],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":136,"issueCount":1189,"starsCount":1619,"forksCount":575,"license":"Other","participation":[0,2,0,6,4,5,5,2,3,0,3,4,2,0,0,0,2,0,0,2,0,0,1,3,1,2,0,9,7,0,0,0,0,1,2,0,1,1,0,1,7,2,2,1,1,3,1,0,3,1,2,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T18:44:37.981Z"}},{"type":"Public","name":"rawls","owner":"broadinstitute","isFork":false,"description":"Rawls service for DSDE","allTopics":[],"primaryLanguage":{"name":"Scala","color":"#c22d40"},"pullRequestCount":11,"issueCount":0,"starsCount":24,"forksCount":3,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[9,11,7,4,11,15,5,6,15,4,11,6,14,3,8,3,3,4,11,5,6,3,5,5,0,2,9,12,7,2,4,8,2,6,2,3,5,3,3,11,5,7,7,13,3,5,9,8,6,3,7,19],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T18:41:24.342Z"}},{"type":"Public","name":"dig-loam-stream","owner":"broadinstitute","isFork":false,"description":"dig-loam-stream","allTopics":[],"primaryLanguage":{"name":"Scala","color":"#c22d40"},"pullRequestCount":0,"issueCount":18,"starsCount":1,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T18:20:07.272Z"}},{"type":"Public","name":"dig-bioindex","owner":"broadinstitute","isFork":false,"description":"BIO index for genetic records stored in S3 and FastAPI server.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":0,"starsCount":6,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[5,0,0,1,0,0,0,2,3,1,5,0,0,2,0,1,0,0,6,4,0,1,0,0,4,0,0,1,0,0,0,0,0,0,0,5,2,0,1,1,0,6,0,0,0,7,1,0,0,0,3,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T18:00:30.305Z"}},{"type":"Public","name":"jump-profiling-recipe","owner":"broadinstitute","isFork":false,"description":"Workflow for processing cpg0016-jump profiles ","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":3,"starsCount":1,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,3,0,3,1,1,7,2,0,0,1,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T17:54:53.787Z"}}],"repositoryCount":1244,"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"}