{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"Clair3-Nova","owner":"HKU-BAL","isFork":false,"description":"de novo variant calling in trio using Nanopore long-reads","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[6,10,0,0,0,15,8,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,6,0,0,0,1,2,0,2,1,3,0,0,0,1,2],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-24T05:56:01.886Z"}},{"type":"Public","name":"ClairS-TO","owner":"HKU-BAL","isFork":false,"description":"ClairS-TO - a deep-learning method for tumor-only somatic variant calling","topicNames":["bioinformatics","deep-learning","nanopore","genomics","somatic-variants","variants","pacbio","variant-calling","somatic-mutations","illumina"],"topicsNotShown":6,"allTopics":["bioinformatics","deep-learning","nanopore","genomics","somatic-variants","variants","pacbio","variant-calling","somatic-mutations","illumina","snvs","long-reads","ont","long-read-sequencing","tumors","tumor-only"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":32,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,4,16,15,7,0,0,0,8,13,0,10,2,0,0,0,0,0,0,0,0,0,0,0,20,0,0,9,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-20T09:31:47.931Z"}},{"type":"Public","name":"Clair3","owner":"HKU-BAL","isFork":false,"description":"Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling","topicNames":["deep-learning","nanopore","genomics","computational-biology","pacbio","variant-calling","illumina","long-reads","variant-detection","ont-data"],"topicsNotShown":1,"allTopics":["deep-learning","nanopore","genomics","computational-biology","pacbio","variant-calling","illumina","long-reads","variant-detection","ont-data","ont-models"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":221,"forksCount":26,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-16T15:55:16.408Z"}},{"type":"Public","name":"ClairS","owner":"HKU-BAL","isFork":false,"description":"ClairS - a deep-learning method for long-read somatic small variant calling","topicNames":["bioinformatics","deep-learning","nanopore","genomics","somatic-variants","haplotypes","pacbio","somatic-mutations","illumina","indels"],"topicsNotShown":6,"allTopics":["bioinformatics","deep-learning","nanopore","genomics","somatic-variants","haplotypes","pacbio","somatic-mutations","illumina","indels","phasing","snvs","long-reads","ont","long-read-sequencing","short-reads"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":6,"starsCount":56,"forksCount":5,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[6,1,0,0,0,4,8,1,0,8,0,16,2,0,0,10,1,0,0,0,0,0,0,2,0,0,0,0,2,1,0,0,0,0,6,0,0,1,0,0,0,0,0,0,0,0,0,16,1,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-04T08:16:53.375Z"}},{"type":"Public","name":"Clair3-RNA","owner":"HKU-BAL","isFork":false,"description":"Clair3-RNA - a long-read small variant caller for RNA sequencing data","topicNames":["rna-seq","deep-learning","nanopore","rna","variant-calling","rna-editing","rna-seq-pipeline","ont","long-read-sequencing","pacbio-iso-seq"],"topicsNotShown":0,"allTopics":["rna-seq","deep-learning","nanopore","rna","variant-calling","rna-editing","rna-seq-pipeline","ont","long-read-sequencing","pacbio-iso-seq"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":8,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,27,0,10,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-19T13:21:16.970Z"}},{"type":"Public archive","name":"Clair3-Trio","owner":"HKU-BAL","isFork":false,"description":"Clair3-Trio: variant calling in trio using Nanopore long-reads","topicNames":["bioinformatics","deep-learning","nanopore","genomics","computational-biology","variant-calling","long-reads","ont-models","trio-variant-calling"],"topicsNotShown":0,"allTopics":["bioinformatics","deep-learning","nanopore","genomics","computational-biology","variant-calling","long-reads","ont-models","trio-variant-calling"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":13,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[6,10,0,0,0,15,8,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,2,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-18T15:20:24.428Z"}},{"type":"Public","name":"ClusterV-Web","owner":"HKU-BAL","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-27T01:30:33.098Z"}},{"type":"Public","name":"ClusterV","owner":"HKU-BAL","isFork":false,"description":"ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data","topicNames":["bioinformatics","nanopore","hiv","nanopore-sequencing","hivdb","subtype-finding"],"topicsNotShown":0,"allTopics":["bioinformatics","nanopore","hiv","nanopore-sequencing","hivdb","subtype-finding"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":7,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,3,2,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-11T09:44:50.930Z"}},{"type":"Public","name":"CellContrast","owner":"HKU-BAL","isFork":false,"description":"CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning","topicNames":["bioinformatics","single-cell-rna-seq","spatial-transcriptomics","contrastive-learning","spatial-reconstruction"],"topicsNotShown":0,"allTopics":["bioinformatics","single-cell-rna-seq","spatial-transcriptomics","contrastive-learning","spatial-reconstruction"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-01T09:34:52.580Z"}},{"type":"Public","name":"Clair3-MP","owner":"HKU-BAL","isFork":false,"description":"variant calling using with sequencing data from multiple platforms","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":4,"forksCount":2,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-14T08:16:07.961Z"}},{"type":"Public","name":"SENSV","owner":"HKU-BAL","isFork":false,"description":"A tool to detect structural variant","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":4,"starsCount":18,"forksCount":3,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-27T09:55:50.894Z"}},{"type":"Public","name":"TC-RENO","owner":"HKU-BAL","isFork":false,"description":"A tool to detect full length isoforms of RNA","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-09T00:59:37.619Z"}},{"type":"Public","name":"CPG","owner":"HKU-BAL","isFork":false,"description":"Building a Chinese pan-genome of 486 individuals","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":12,"forksCount":5,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-23T09:01:09.474Z"}},{"type":"Public","name":"AF-NS","owner":"HKU-BAL","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-23T08:59:59.123Z"}},{"type":"Public","name":"ONT-TB-NF","owner":"HKU-BAL","isFork":false,"description":"Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.","topicNames":["bioinformatics","nanopore","bioinformatics-pipeline","mycobacterium-tuberculosis","nanopore-analysis-pipeline","adaptive-sequencing"],"topicsNotShown":0,"allTopics":["bioinformatics","nanopore","bioinformatics-pipeline","mycobacterium-tuberculosis","nanopore-analysis-pipeline","adaptive-sequencing"],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":1,"starsCount":5,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-22T05:43:05.701Z"}},{"type":"Public","name":"CONNET","owner":"HKU-BAL","isFork":false,"description":"CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning","topicNames":["bioinformatics","computational-biology","genome-assembly","deep-learning","consensus"],"topicsNotShown":0,"allTopics":["bioinformatics","computational-biology","genome-assembly","deep-learning","consensus"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":4,"starsCount":12,"forksCount":6,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-28T12:47:52.775Z"}},{"type":"Public","name":"Clair","owner":"HKU-BAL","isFork":false,"description":"Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling","topicNames":["bioinformatics","deep-learning","computational-biology","variant-calling"],"topicsNotShown":0,"allTopics":["bioinformatics","deep-learning","computational-biology","variant-calling"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":2,"starsCount":102,"forksCount":12,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-09-01T07:38:03.910Z"}},{"type":"Public","name":"MegaPath-Nano","owner":"HKU-BAL","isFork":false,"description":"MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics; MegaPath-Nano-Amplicon: filtering module for metagenomic amplicon data","topicNames":["ont","taxonomic-analysis","amr-detection"],"topicsNotShown":0,"allTopics":["ont","taxonomic-analysis","amr-detection"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":1,"starsCount":15,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-02T03:36:06.890Z"}},{"type":"Public","name":"ECNano","owner":"HKU-BAL","isFork":false,"description":"A target captured medical exome ONT sequencing with amplicon variant calling workflow","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":6,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-03-08T14:38:43.098Z"}},{"type":"Public","name":"MegaPath","owner":"HKU-BAL","isFork":false,"description":"MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data","topicNames":["filter","ngs","metagenomics","amplicon","taxonomic-classification"],"topicsNotShown":0,"allTopics":["filter","ngs","metagenomics","amplicon","taxonomic-classification"],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":3,"starsCount":6,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-10T04:02:04.975Z"}},{"type":"Public","name":"HKG","owner":"HKU-BAL","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-11T13:51:14.862Z"}},{"type":"Public","name":"Chromatin-Fiber-Imaging","owner":"HKU-BAL","isFork":false,"description":"Chromatin Fiber Imaging","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-07-30T03:51:54.275Z"}},{"type":"Public","name":"ncov19_cytosine_depletion","owner":"HKU-BAL","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":"2020-12-11T08:10:08.529Z"}},{"type":"Public","name":"ChromSeg","owner":"HKU-BAL","isFork":false,"description":"A framework for crossing-overlap chromosome segmentation","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":7,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-10-23T06:46:06.887Z"}},{"type":"Public","name":"UNCALLED","owner":"HKU-BAL","isFork":false,"description":"Raw nanopore signal mapper that enables real-time targeted sequencing","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-09-07T04:34:12.979Z"}},{"type":"Public","name":"Translocator","owner":"HKU-BAL","isFork":false,"description":"Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":1,"starsCount":13,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-01-22T02:50:44.465Z"}},{"type":"Public","name":"Clairvoyante-PyTroch","owner":"HKU-BAL","isFork":false,"description":"Pytorch version of Clairvoyante","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":9,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-02-28T04:21:52.788Z"}},{"type":"Public","name":"MegaGTA","owner":"HKU-BAL","isFork":false,"description":"HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":17,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-10-03T08:30:18.361Z"}},{"type":"Public","name":"megabox","owner":"HKU-BAL","isFork":false,"description":"A web platform for hosting up-to-date MEGAHIT assemblies of publicly available but challenging metagenome sequence data.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"CSS","color":"#563d7c"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-03-29T08:46:19.727Z"}}],"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":"Repositories"}