{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"MSTmap-Python","owner":"ucrbioinfo","isFork":true,"description":"A Python wrapper for UCRBioInfo MSTmap","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-27T21:12:28.851Z"}},{"type":"Public","name":"rambler","owner":"ucrbioinfo","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-13T00:50:16.148Z"}},{"type":"Public","name":"allegro","owner":"ucrbioinfo","isFork":true,"description":"ALLEGRO: An Algorithm Leveraging Linear Programing to Enhance Guide RNA Optimization","allTopics":["synthetic-biology","linear-programming","combinatorial-optimization","crispr-cas9","genome-editing","crispr-design"],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-31T01:08:03.498Z"}},{"type":"Public","name":"deepguide_reborn","owner":"ucrbioinfo","isFork":false,"description":"A reimplementation of the original <a href=\"https://github.com/dDipankar/DeepGuide\">https://github.com/dDipankar/DeepGuide</a> by Dipankar Ranjan Baisya","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-06T17:07:43.087Z"}},{"type":"Public","name":"Fugue","owner":"ucrbioinfo","isFork":true,"description":"FUGUE is a preprocessing tool for ALLEGRO","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-02T19:10:29.141Z"}},{"type":"Public","name":"dmc_prediction","owner":"ucrbioinfo","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-20T04:53:39.492Z"}},{"type":"Public","name":"fosinopril","owner":"ucrbioinfo","isFork":false,"description":"Software for \"In Vitro Antibabesial Activity of the ACE Inhibitor Fosinopril Requires Drug Activation by a Parasite Esterase BdFE1 \"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-21T20:50:58.209Z"}},{"type":"Public","name":"AMPS","owner":"ucrbioinfo","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-05T05:53:50.423Z"}},{"type":"Public","name":"GeneLocalizationBduncani","owner":"ucrbioinfo","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-05-17T23:11:57.695Z"}},{"type":"Public","name":"DeepGuide","owner":"ucrbioinfo","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-24T03:07:45.912Z"}},{"type":"Public","name":"PGV","owner":"ucrbioinfo","isFork":false,"description":"Reference-agnostic Representation and Visualization of Pan-genomes","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":18,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-09-16T19:13:14.509Z"}},{"type":"Public","name":"MSTmap","owner":"ucrbioinfo","isFork":false,"description":"A software tool that builds genetic linkage maps efficiently and accurately","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":0,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-07-30T20:59:52.366Z"}},{"type":"Public","name":"MergeMap","owner":"ucrbioinfo","isFork":false,"description":"MergeMap is a software tool that builds accurate consensus genetic maps from a set of individual genetic maps","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-07T15:52:21.292Z"}},{"type":"Public","name":"cowpea_pangenome","owner":"ucrbioinfo","isFork":false,"description":"Companion website to cowpea pangenome paper","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-03-18T18:49:18.991Z"}},{"type":"Public","name":"DeeplyEssential","owner":"ucrbioinfo","isFork":false,"description":"Deep neural network based prediction model for gene essentiality prediction in microbes","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":9,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-02-11T03:27:22.782Z"}},{"type":"Public","name":"SELFISH","owner":"ucrbioinfo","isFork":false,"description":"Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure","allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":2,"starsCount":3,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-11-18T22:12:53.741Z"}},{"type":"Public","name":"Epi2En","owner":"ucrbioinfo","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-11-04T20:36:46.607Z"}},{"type":"Public","name":"Novo_Stitch","owner":"ucrbioinfo","isFork":false,"description":"Novo&amp;Stitch is a genome assembly reconciliation tool based on optical map.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":10,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-10-21T18:51:23.221Z"}},{"type":"Public","name":"DeepHistone","owner":"ucrbioinfo","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-02-02T02:25:58.630Z"}},{"type":"Public","name":"OMGS","owner":"ucrbioinfo","isFork":false,"description":"OMGS is a fast and accurate genome scaffolding tool with one or multiple Bionano optical maps ","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":7,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-11-04T01:42:51.035Z"}},{"type":"Public","name":"Chimericognizer","owner":"ucrbioinfo","isFork":false,"description":"Chimericognizer is a novel and accurate chimeric contigs correction tool based on optical maps.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":8,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-06-10T23:33:47.592Z"}},{"type":"Public","name":"XMView","owner":"ucrbioinfo","isFork":false,"description":"A Multiple Alignment XMap Viewer with Genetic Map Integration ","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-01-15T21:29:48.800Z"}},{"type":"Public","name":"EAST","owner":"ucrbioinfo","isFork":false,"description":"EAST: Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-11T07:13:57.088Z"}},{"type":"Public","name":"ThIEF","owner":"ucrbioinfo","isFork":false,"description":"Finding Genome-wide Trajectories of Epigenetics Marks","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-01-27T03:50:19.701Z"}},{"type":"Public","name":"FMTP","owner":"ucrbioinfo","isFork":false,"description":"Fingerprint-based Minimal Tiling Path ","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-08-07T21:51:55.798Z"}},{"type":"Public","name":"BRAT_nova","owner":"ucrbioinfo","isFork":false,"description":"Fast and accurate mapping of bisulfite-treated reads","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-08-01T03:56:17.261Z"}},{"type":"Public","name":"PuFFIN","owner":"ucrbioinfo","isFork":false,"description":"A Parameter-free Method to Build Genome-wide Nucleosome Maps from Paired-end Sequencing Data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-07-30T21:52:57.525Z"}},{"type":"Public","name":"NOrMAL","owner":"ucrbioinfo","isFork":false,"description":"Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-07-28T18:31:32.497Z"}},{"type":"Public","name":"LRTag","owner":"ucrbioinfo","isFork":false,"description":"LRTag is a tool that is capable of efficiently selecting a near optimal set of SNP markers across multiple populations.","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-07-28T18:25:26.377Z"}}],"repositoryCount":29,"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":"ucrbioinfo repositories"}