{"payload":{"pageCount":3,"repositories":[{"type":"Public","name":"pangraph","owner":"neherlab","isFork":false,"description":"A bioinformatic toolkit to align genome assemblies into pangenome graphs","topicNames":["genome","bacteria","genome-assembly","pangenome","pangraph","bioinformatics","julia"],"topicsNotShown":0,"primaryLanguage":{"name":"Julia","color":"#a270ba"},"pullRequestCount":2,"issueCount":8,"starsCount":74,"forksCount":6,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-30T13:56:02.690Z"}},{"type":"Public","name":"nextclade_data_workflows","owner":"neherlab","isFork":false,"description":"","topicNames":["snakemake","phylogenetics","nextstrain","virus-evolution","nextclade"],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":10,"starsCount":4,"forksCount":1,"license":null,"participation":[13,4,7,7,1,7,1,3,2,2,3,0,11,12,5,7,3,4,5,3,5,2,0,12,1,0,0,1,0,7,9,13,1,0,0,3,20,1,0,3,2,0,2,2,0,2,2,4,2,2,0,3],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-26T14:18:31.958Z"}},{"type":"Public","name":"treetime","owner":"neherlab","isFork":false,"description":"Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction","topicNames":["phylogenetics"],"topicsNotShown":0,"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":3,"issueCount":27,"starsCount":205,"forksCount":54,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-24T07:53:22.325Z"}},{"type":"Public","name":"SARS-CoV-2_variant-reports","owner":"neherlab","isFork":false,"description":"Informal summaries of notable SARS-CoV-2 lineages","topicNames":["covid-19","sars-cov-2","virus-evolution","sars-cov-2-variants"],"topicsNotShown":0,"primaryLanguage":null,"pullRequestCount":3,"issueCount":2,"starsCount":102,"forksCount":11,"license":null,"participation":[0,0,0,2,0,0,0,0,2,0,0,1,0,0,0,1,1,1,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,4,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-05T13:02:55.646Z"}},{"type":"Public","name":"simple-annotator","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-29T08:08:58.968Z"}},{"type":"Public","name":"HIV-nextclade","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,9,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,6,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-18T20:30:41.726Z"}},{"type":"Public","name":"spike-only","owner":"neherlab","isFork":false,"description":"Spike-only SARS-CoV-2 Nextstrain build","topicNames":["bioinformatics","phylogenetics","augur","nextstrain","sars-cov-2","nextstrain-ncov","sars-cov-2-variants"],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-13T17:58:33.259Z"}},{"type":"Public","name":"BA286","owner":"neherlab","isFork":false,"description":"BA.2.86 project with Sigal lab","topicNames":["bioinformatics","snakemake","computational-biology","phylogenetics","nextstrain","treetime","sars-cov-2","virus-evolution","genomic-epidemiology","sars-cov-2-variants"],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":2,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-08T09:50:58.950Z"}},{"type":"Public","name":"pan-genome-analysis","owner":"neherlab","isFork":false,"description":"Processing pipeline for pan-genome visulization and exploration","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":33,"starsCount":127,"forksCount":37,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-09T13:23:45.828Z"}},{"type":"Public","name":"RSV_nextclade_trial","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-03T16:29:21.659Z"}},{"type":"Public","name":"nextclade_data","owner":"neherlab","isFork":true,"description":"DO NOT USE. This is for testing new stuff on <a href=\"https://github.com/nextstrain/nextclade_data\">https://github.com/nextstrain/nextclade_data</a>","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":18,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-28T17:40:37.713Z"}},{"type":"Public","name":"ncov-simple","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":9,"starsCount":2,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-24T15:09:01.491Z"}},{"type":"Public","name":"flu_clades","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-23T15:50:04.506Z"}},{"type":"Public","name":"outlier-detection","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-11T17:04:32.519Z"}},{"type":"Public","name":"minimizer","owner":"neherlab","isFork":true,"description":"Rust implementation of a minimizer index","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Rust","color":"#dea584"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-05T14:57:13.992Z"}},{"type":"Public","name":"sc2-phylo-workflow","owner":"neherlab","isFork":false,"description":"demonstraion workflow for SC2 phylogenetic analysis using nextclade","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-01T14:46:53.199Z"}},{"type":"Public","name":"ffpopsim","owner":"neherlab","isFork":false,"description":"FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter i…","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":1,"issueCount":2,"starsCount":12,"forksCount":11,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-17T04:24:39.094Z"}},{"type":"Public","name":"Rpi_test_tools","owner":"neherlab","isFork":false,"description":"Scripts to test the Rpi for the morbidostat","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-07T09:23:56.081Z"}},{"type":"Public","name":"flu-ingest","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-09T08:33:55.251Z"}},{"type":"Public","name":"CompBio2023","owner":"neherlab","isFork":false,"description":"simple viral consensus assembly","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-24T12:08:39.898Z"}},{"type":"Public","name":"TreeKnit-web","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"TypeScript","color":"#3178c6"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-21T19:16:08.396Z"}},{"type":"Public","name":"SC2_variant_rates","owner":"neherlab","isFork":false,"description":"analyze substitution rate and mutation behavior within variants. ","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-12T08:03:43.347Z"}},{"type":"Public","name":"pan-genome-visualization","owner":"neherlab","isFork":true,"description":"Visualization of the pan-genome output by panX","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":2,"issueCount":7,"starsCount":59,"forksCount":22,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-07T17:01:05.045Z"}},{"type":"Public","name":"nextclade-dataset-template","owner":"neherlab","isFork":false,"description":"Template to create a simple Nextclade dataset from scratch","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-21T17:11:09.229Z"}},{"type":"Public","name":"pangraph-paper","owner":"neherlab","isFork":false,"description":"latex source files for the pangraph paper","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-16T17:26:44.348Z"}},{"type":"Public","name":"nextclade_testing_gffs","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-07T15:12:31.946Z"}},{"type":"Public","name":"h5NCtest","owner":"neherlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-20T14:32:10.398Z"}},{"type":"Public","name":"HIVEVO_reversion","owner":"neherlab","isFork":false,"description":"Repository for the analysis and figures of Valentin Druelle's paper on HIV-1 reversion","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-10T09:04:26.680Z"}},{"type":"Public","name":"python_morbidostat","owner":"neherlab","isFork":false,"description":"Control software for a morbidostat reactor based on arduino and python","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":5,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-08T16:29:42.809Z"}},{"type":"Public","name":"SVVC","owner":"neherlab","isFork":false,"description":"simple viral variant caller","topicNames":[],"topicsNotShown":0,"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-20T07:15:13.344Z"}}],"repositoryCount":79,"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":"mirror","text":"Mirrors"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}