{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"EM-seq","owner":"nebiolabs","isFork":false,"description":"Tools and Data related to Enzymatic Methylation Sequencing","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":5,"starsCount":13,"forksCount":2,"license":"GNU Affero General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-19T01:26:59.615Z"}},{"type":"Public","name":"domainator","owner":"nebiolabs","isFork":false,"description":"A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":13,"starsCount":8,"forksCount":0,"license":"Other","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,9,2,0,1,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-15T14:17:28.226Z"}},{"type":"Public","name":"domainator_examples","owner":"nebiolabs","isFork":false,"description":"Advanced examples of how to use the Domainator bioinformatics software suite","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,2,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-24T13:30:24.233Z"}},{"type":"Public","name":"ampseer","owner":"nebiolabs","isFork":false,"description":"Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.","topicNames":["sequencing","pcr","targeted-sequencing","sars-cov-2"],"topicsNotShown":0,"allTopics":["sequencing","pcr","targeted-sequencing","sars-cov-2"],"primaryLanguage":{"name":"Rust","color":"#dea584"},"pullRequestCount":0,"issueCount":5,"starsCount":12,"forksCount":1,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-27T09:23:24.398Z"}},{"type":"Public","name":"fatools","owner":"nebiolabs","isFork":true,"description":"A Python library for performing DNA fragment-analysis","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":10,"license":"GNU Lesser General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-07T18:18:07.705Z"}},{"type":"Public","name":"tasmanian-mismatch","owner":"nebiolabs","isFork":false,"description":"Analysis of artifacts in high throughput sequencing data from genomic DNA. ","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":2,"issueCount":7,"starsCount":1,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-04T17:39:08.076Z"}},{"type":"Public","name":"unclePy","owner":"nebiolabs","isFork":false,"description":"A parser for Unchained Labs Uncle HDF5 binary files written in Python.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":4,"starsCount":0,"forksCount":1,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-21T16:52:53.331Z"}},{"type":"Public","name":"uncleShiny","owner":"nebiolabs","isFork":false,"description":"A dashboard for Unchained Labs Uncle data visualization written in R using Shiny.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":6,"starsCount":0,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-15T16:44:30.586Z"}},{"type":"Public","name":"opentrons","owner":"nebiolabs","isFork":false,"description":"Collection of scripts which can be used in relation to Opentrons OT-2 Liquid Handling Robot","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-03T17:21:29.730Z"}},{"type":"Public","name":"plate-map","owner":"nebiolabs","isFork":false,"description":"A flexible tool for defining the contents of 96 well plates.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":5,"issueCount":7,"starsCount":45,"forksCount":13,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-12T18:49:37.177Z"}},{"type":"Public","name":"mark-nonconverted-reads","owner":"nebiolabs","isFork":false,"description":"This program examines a BAM or SAM stream for reads that contain multiple Cs in non-CpG context. It markes these reads with a tag (XX:Z:UC) and sets the vendor failed bit to prevent these reads from being used in downstream methylation calling. It also prints summary information to stderr.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":2,"forksCount":1,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-16T14:56:56.699Z"}},{"type":"Public","name":"picard_bcl_to_fastq","owner":"nebiolabs","isFork":false,"description":"Demultiplexes a MiSeq, NextSeq or HiSeq run using Picard's IlluminaBasecallsToFastq","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-28T14:22:46.967Z"}},{"type":"Public","name":"formtastic","owner":"nebiolabs","isFork":true,"description":"A Rails form builder plugin with semantically rich and accessible markup.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Ruby","color":"#701516"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":630,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-06T15:53:10.227Z"}},{"type":"Public","name":"low_bismap_methyl_calls","owner":"nebiolabs","isFork":false,"description":"Tools to assess called methylation in low mappability regions (as defined by bismap). Aligner MapQ does not always align with low mappability","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":4,"starsCount":0,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-29T16:51:57.275Z"}},{"type":"Public","name":"seq-results-deprecated","owner":"nebiolabs","isFork":false,"description":"Deprecated: Web interface to manage a database of sequence results (merged into ngs-aggregate-results)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Ruby","color":"#701516"},"pullRequestCount":9,"issueCount":2,"starsCount":1,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-14T05:24:23.131Z"}},{"type":"Public","name":"iwc","owner":"nebiolabs","isFork":true,"description":"Intergalactic Workflow Commission","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":52,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-05T14:19:39.883Z"}},{"type":"Public","name":"poreCov","owner":"nebiolabs","isFork":true,"description":"SARS-CoV-2 workflow for nanopore sequence data","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":15,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-23T16:01:12.201Z"}},{"type":"Public","name":"neb-galaxy-workflows","owner":"nebiolabs","isFork":false,"description":"Galaxy Workflows ","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-19T18:35:25.998Z"}},{"type":"Public","name":"usegalaxy-tools","owner":"nebiolabs","isFork":true,"description":"usegalaxy.* common tools","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":46,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-11T18:53:29.448Z"}},{"type":"Public","name":"VarSkip","owner":"nebiolabs","isFork":false,"description":"VarSkip multiplex PCR designs for SARS-CoV-2 sequencing","topicNames":["sequencing","pcr","sars-cov-2"],"topicsNotShown":0,"allTopics":["sequencing","pcr","sars-cov-2"],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":11,"forksCount":9,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-14T17:01:14.316Z"}},{"type":"Public","name":"datasets-sars-cov-2","owner":"nebiolabs","isFork":true,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Perl","color":"#0298c3"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":16,"license":"Apache License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-10T19:10:24.674Z"}},{"type":"Public","name":"artic-ncov2019","owner":"nebiolabs","isFork":true,"description":"ARTIC nanopore protocol for nCoV2019 novel coronavirus","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":167,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-16T12:38:48.209Z"}},{"type":"Public","name":"Cas-PAM-cleavage-analysis","owner":"nebiolabs","isFork":true,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-06T15:21:55.017Z"}},{"type":"Public","name":"primer-schemes","owner":"nebiolabs","isFork":true,"description":"Primer schemes for real-time genome epidemiology","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":42,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-07-10T18:42:32.489Z"}},{"type":"Public","name":"ngslite","owner":"nebiolabs","isFork":true,"description":"Light-weight functions for next-generation sequencing (NGS) data analysis","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-15T15:37:20.671Z"}},{"type":"Public","name":"galaxytools","owner":"nebiolabs","isFork":true,"description":"🔬📚 Galaxy Tool wrappers","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":217,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-12-18T21:25:09.051Z"}},{"type":"Public","name":"bwa-meth","owner":"nebiolabs","isFork":true,"description":"fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"PostScript","color":"#da291c"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":54,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-12-07T15:44:17.538Z"}},{"type":"Public","name":"Bismark","owner":"nebiolabs","isFork":true,"description":"A tool to map bisulfite converted sequence reads and determine cytosine methylation states","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":102,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-12-04T14:07:30.312Z"}},{"type":"Public","name":"checkQC","owner":"nebiolabs","isFork":true,"description":"CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":16,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-10-13T13:28:58.140Z"}},{"type":"Public","name":"nebnext-single-cell-rna-seq","owner":"nebiolabs","isFork":false,"description":"Adapter trimming directions for NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":2,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-07-13T21:27:00.427Z"}}],"repositoryCount":52,"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"}