{"payload":{"pageCount":4,"repositories":[{"type":"Public","name":"larch","owner":"matsengrp","isFork":false,"description":"Inference and manipulation of history DAGs","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":3,"issueCount":14,"starsCount":2,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-24T15:19:40.613Z"}},{"type":"Public","name":"multidms","owner":"matsengrp","isFork":false,"description":"Joint modeling of multiple deep mutational scanning experiments","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":18,"starsCount":1,"forksCount":0,"license":"MIT License","participation":[0,5,0,0,2,1,9,43,2,4,0,5,0,0,0,0,0,0,0,3,0,1,2,0,0,0,1,3,0,0,0,0,0,0,0,6,0,0,5,1,0,8,2,0,0,1,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-23T18:07:39.023Z"}},{"type":"Public","name":"gctree","owner":"matsengrp","isFork":false,"description":"GCtree: phylogenetic inference of genotype-collapsed trees","topicNames":["phylogenetics","single-cell"],"topicsNotShown":0,"allTopics":["phylogenetics","single-cell"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":14,"starsCount":16,"forksCount":2,"license":"GNU General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0,0,1,0,0,0,0,2,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-20T21:00:30.211Z"}},{"type":"Public","name":"dnsm-json-database","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,1,1,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-17T20:04:23.213Z"}},{"type":"Public","name":"antigen","owner":"matsengrp","isFork":true,"description":"Simulating virus evolution and epidemiology","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Mathematica","color":"#dd1100"},"pullRequestCount":2,"issueCount":4,"starsCount":1,"forksCount":8,"license":null,"participation":[0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-17T00:45:44.798Z"}},{"type":"Public","name":"historydag","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":12,"starsCount":0,"forksCount":1,"license":"GNU General Public License v3.0","participation":[0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,9,0,0,0,1,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-16T21:12:08.064Z"}},{"type":"Public","name":"LASV-manuscript-nextstrain-dmsa","owner":"matsengrp","isFork":false,"description":"This repository holds the build code for generating a nextstrain tree with escape score predictions.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-23T16:36:45.440Z"}},{"type":"Public","name":"lassa-dmsa","owner":"matsengrp","isFork":true,"description":"Nextstrain build for Lassa virus","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":4,"license":null,"participation":[0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,1,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-22T20:47:22.869Z"}},{"type":"Public","name":"dmsa-pred","owner":"matsengrp","isFork":false,"description":"A standalone package for using deep mutational scanning data to predict the phenotypes of untested sequences from a multiple-sequence alignment.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-16T22:28:33.783Z"}},{"type":"Public","name":"bcr-phylo-benchmark","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":3,"starsCount":3,"forksCount":8,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-10T16:13:38.236Z"}},{"type":"Public","name":"seasonal-flu-dmsa","owner":"matsengrp","isFork":true,"description":"Fork of seasonal-flu nextstrain build to include phenotype predictions informed by dms data.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":24,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-31T21:50:41.437Z"}},{"type":"Public","name":"phip-flow","owner":"matsengrp","isFork":false,"description":"A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":2,"starsCount":8,"forksCount":5,"license":"MIT License","participation":[0,1,1,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-15T13:52:35.436Z"}},{"type":"Public","name":"SARS-CoV-2_spike_multidms","owner":"matsengrp","isFork":false,"description":"Comparing DMS datasets for spike from Delta, Omicron BA.1, and Omicron BA.2 ","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":[1,1,9,9,2,2,3,7,21,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-13T23:03:53.431Z"}},{"type":"Public","name":"linearham","owner":"matsengrp","isFork":false,"description":"A Bayesian Phylo-HMM for B cell receptor sequence analysis","topicNames":["phylogenetics","immunology","b-cell"],"topicsNotShown":0,"allTopics":["phylogenetics","immunology","b-cell"],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":2,"issueCount":4,"starsCount":6,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T22:58:03.910Z"}},{"type":"Public","name":"SARS-CoV-2-S2-Abs","owner":"matsengrp","isFork":false,"description":"Repository for Antibody Responses to SARS-CoV-2 S2 manuscript","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-28T18:46:40.003Z"}},{"type":"Public","name":"phippery","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":12,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-23T20:38:23.973Z"}},{"type":"Public","name":"hdag-benchmark","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":0,"forksCount":0,"license":null,"participation":[0,6,0,0,9,1,0,0,0,1,0,0,0,0,4,0,0,0,0,0,0,0,2,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-11T18:09:53.512Z"}},{"type":"Public","name":"infection-timing","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-07T21:42:36.885Z"}},{"type":"Public","name":"usher","owner":"matsengrp","isFork":true,"description":"Ultrafast Sample Placement on Existing Trees","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":40,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-03T16:09:55.580Z"}},{"type":"Public","name":"CYP-multidms","owner":"matsengrp","isFork":false,"description":"a repository for the analysis of C9 and C19 dms data","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,3,1,1,0,0,3,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-04T17:26:13.711Z"}},{"type":"Public template","name":"tex-template","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-31T19:31:28.806Z"}},{"type":"Public","name":"LK-SARS-CoV-2","owner":"matsengrp","isFork":false,"description":"Repository for Linda Kizazi SARS-CoV-2 manuscript Analysis","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-28T04:00:26.608Z"}},{"type":"Public","name":"zika-dmsa","owner":"matsengrp","isFork":true,"description":"Nextstrain build for Zika virus with dms model phenotype predictions","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":9,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-18T16:50:58.015Z"}},{"type":"Public","name":"sumrep","owner":"matsengrp","isFork":false,"description":"Summary statistics for repertoires","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":2,"issueCount":15,"starsCount":16,"forksCount":6,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-01T18:33:50.263Z"}},{"type":"Public","name":"olmsted","owner":"matsengrp","isFork":false,"description":"B-cell repertoire and clonal family tree explorer","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":26,"issueCount":60,"starsCount":15,"forksCount":4,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-23T17:40:00.157Z"}},{"type":"Public","name":"gp-benchmark-1","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-30T16:59:07.695Z"}},{"type":"Public","name":"gp-benchmark-1-environment","owner":"matsengrp","isFork":false,"description":"Code to explore to what extent GP composite likelihoods and their derivatives correspond to more well-understood quantities","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":3,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-29T19:00:59.496Z"}},{"type":"Public","name":"usher-clade-reconstructions","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-16T21:26:24.931Z"}},{"type":"Public","name":"find-dnapars-trees","owner":"matsengrp","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-28T22:46:41.370Z"}},{"type":"Public","name":"vbpi-torch","owner":"matsengrp","isFork":true,"description":"Pytorch Implementation of Variational Bayesian Phylogenetic Inference","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-15T17:54:53.796Z"}}],"repositoryCount":101,"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"}