{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"GenCHORD","owner":"wtsi-hpag","isFork":false,"description":"A Bayesian method to smooth-out the noise in a coverage dataset, revealing the underlying average behaviour which is constrained to lie on `Harmonics' of a fundamental coverage value.","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":11,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-09T14:06:39.839Z"}},{"type":"Public","name":"CoverageWorkshop","owner":"wtsi-hpag","isFork":false,"description":"A Workshop Notebook used for running a session as part of the OpenLab series.","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-12T10:54:43.276Z"}},{"type":"Public","name":"stepStone","owner":"wtsi-hpag","isFork":false,"description":"A pipeline for identification of chromothripsis breakpoints and cancer rearrangements","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-22T20:42:15.269Z"}},{"type":"Public","name":"HypoCoverage","owner":"wtsi-hpag","isFork":false,"description":"Coverage Analysis Tools","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-10T13:39:16.430Z"}},{"type":"Public","name":"MCSampler","owner":"wtsi-hpag","isFork":false,"description":"An MCMC Sampling framework for sampling from arbitrary probability densities. ","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-18T10:34:47.901Z"}},{"type":"Public","name":"scaffHiC","owner":"wtsi-hpag","isFork":false,"description":"Pipeline for genome scaffolding by modelling distributions of HiC pairs","allTopics":["bioinformatics","hic-analysis","hic-qc","genome-scaffolding"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":3,"starsCount":10,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-07T11:09:29.038Z"}},{"type":"Public","name":"HypothesisTester","owner":"wtsi-hpag","isFork":false,"description":"A Bayesian Statistical Inference framework for comparing hypotheses","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-18T11:00:43.487Z"}},{"type":"Public","name":"ContactPointAnalysis","owner":"wtsi-hpag","isFork":false,"description":"A statistical tool for analysing the Contact Point hypothesis for Chromothripsis","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-26T18:20:57.006Z"}},{"type":"Public","name":"Scaff10X","owner":"wtsi-hpag","isFork":false,"description":"Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads","allTopics":["bioinformatics","genomics","genome","assembly","scaffolding","breaking","10xgenomics"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":3,"issueCount":24,"starsCount":20,"forksCount":4,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-02T03:11:18.502Z"}},{"type":"Public","name":"chromoSPA","owner":"wtsi-hpag","isFork":false,"description":"A Size and Positional Analysis (SPA) tool for studying chromothripsis breakages.","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-28T15:49:50.067Z"}},{"type":"Public","name":"scaffhtag","owner":"wtsi-hpag","isFork":false,"description":"Pipeline for scaffolding genome assemblies using haplotagging reads","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-05-17T14:41:39.963Z"}},{"type":"Public","name":"LinkStats","owner":"wtsi-hpag","isFork":false,"description":"Collect and process statistics from aligned linked-reads.","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-17T10:48:33.346Z"}},{"type":"Public","name":"HiLine","owner":"wtsi-hpag","isFork":false,"description":"HiC alignment and classification pipeline","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":4,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-10-08T14:43:15.222Z"}},{"type":"Public","name":"SamHaplotag","owner":"wtsi-hpag","isFork":false,"description":"Process haplotag barcodes in SAM format","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-29T12:01:10.971Z"}},{"type":"Public","name":"caus","owner":"wtsi-hpag","isFork":false,"description":"CAUS is a pipeline for Chromosome Assignment Using Synteny","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":2,"starsCount":4,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-05-17T16:32:00.940Z"}},{"type":"Public","name":"easyChain","owner":"wtsi-hpag","isFork":false,"description":"easyChain is a pipeline to produce a chain file from two genome assemblies.","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-03-09T17:17:33.252Z"}},{"type":"Public","name":"covidPileup","owner":"wtsi-hpag","isFork":false,"description":"Pipeline for building SNP and GAP pileup from multiple COVID-19 whole genome sequences.","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-06-30T09:09:48.554Z"}},{"type":"Public","name":"varibase","owner":"wtsi-hpag","isFork":false,"description":"A pipeline to correct variation errors of SNPs/indles from genome assembly","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-05-04T14:59:12.698Z"}},{"type":"Public","name":"SIMDExtensionWrapper","owner":"wtsi-hpag","isFork":false,"description":"Generic wrapper program, detects SIMD CPU extensions and launches an appropriate sub-process.","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-11-20T12:04:33.507Z"}},{"type":"Public","name":"AncesBin","owner":"wtsi-hpag","isFork":false,"description":"Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies","allTopics":["genome-assembly","10x","ont","genome-ancestry","reads-binning","pacbio","hic"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-10-14T16:07:39.942Z"}},{"type":"Public","name":"scanPAV","owner":"wtsi-hpag","isFork":false,"description":"Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.","allTopics":["bioinformatics","genomics","bioinformatics-pipeline","structurevariation","genomes-comparison","genome-mapping","pipeline","fasta","smalt","genome-alignment","pav-sequences"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":3,"starsCount":29,"forksCount":7,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-03-05T09:57:45.190Z"}},{"type":"Public","name":"smis","owner":"wtsi-hpag","isFork":true,"description":"SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)","allTopics":["genome","assembly","pacbio","scaffolding","long-reads","ont","oxfordnanopore"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":2,"starsCount":4,"forksCount":2,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-02-19T14:17:54.241Z"}}],"repositoryCount":22,"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":"wtsi-hpag repositories"}