{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"MINTIE","owner":"Oshlack","isFork":false,"description":"Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.","allTopics":["rna-seq","transcriptomics","structural-variation","duplications","rare-disease","gene-fusions","cryptic-variants","cancer"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":33,"forksCount":7,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-01T23:59:14.755Z"}},{"type":"Public","name":"missMethyl","owner":"Oshlack","isFork":false,"description":"Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":5,"starsCount":10,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-19T01:53:19.604Z"}},{"type":"Public","name":"ALLSorts","owner":"Oshlack","isFork":false,"description":"ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":4,"starsCount":15,"forksCount":7,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-17T23:18:08.973Z"}},{"type":"Public","name":"oshlack.github.io","owner":"Oshlack","isFork":false,"description":"Oshlack Lab website","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":1,"issueCount":0,"starsCount":2,"forksCount":5,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-09T04:55:38.283Z"}},{"type":"Public","name":"splatter","owner":"Oshlack","isFork":false,"description":"Simple simulation of single-cell RNA sequencing data","allTopics":["bioinformatics","scrna-seq","simulation","bioconductor"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":6,"starsCount":210,"forksCount":56,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-06T11:41:18.590Z"}},{"type":"Public","name":"Damsel","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-16T04:58:45.977Z"}},{"type":"Public","name":"xenanoseq","owner":"Oshlack","isFork":true,"description":"Nanopore demultiplexing, QC and alignment pipeline for xenograph RNA-seq experiments","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":76,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-17T02:36:17.674Z"}},{"type":"Public","name":"TALLSorts","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-08T09:11:58.331Z"}},{"type":"Public","name":"hashtag-demux-paper","owner":"Oshlack","isFork":false,"description":"Analysis code for \"Benchmarking single-cell hashtag oligo demultiplexing methods\" paper","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-25T04:49:35.118Z"}},{"type":"Public","name":"TobleroneApp","owner":"Oshlack","isFork":false,"description":"Desktop app incorporating https://github.com/oshlack/toblerone","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-24T05:03:43.452Z"}},{"type":"Public","name":"Toblerone","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Rust","color":"#dea584"},"pullRequestCount":0,"issueCount":2,"starsCount":4,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-24T04:45:08.016Z"}},{"type":"Public","name":"Clinker","owner":"Oshlack","isFork":false,"description":"Gene Fusion Visualiser","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":17,"starsCount":50,"forksCount":12,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-15T13:49:06.651Z"}},{"type":"Public","name":"paed-cf-cite-seq","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-23T04:48:03.416Z"}},{"type":"Public","name":"methyl-geneset-testing","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":1,"starsCount":7,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-18T04:00:52.479Z"}},{"type":"Public","name":"TopDeck","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-21T07:34:42.141Z"}},{"type":"Public","name":"speckle","owner":"Oshlack","isFork":false,"description":"R package for specialised analysis of single cell data","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":7,"starsCount":35,"forksCount":5,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-14T05:55:57.791Z"}},{"type":"Public","name":"JAFFA","owner":"Oshlack","isFork":false,"description":"JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":9,"starsCount":80,"forksCount":20,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-24T08:13:55.882Z"}},{"type":"Public","name":"Slinker","owner":"Oshlack","isFork":false,"description":"Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":18,"forksCount":4,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-13T14:50:49.014Z"}},{"type":"Public","name":"Corset","owner":"Oshlack","isFork":false,"description":"Software for clustering de novo assembled transcripts and counting overlapping reads","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":4,"starsCount":68,"forksCount":18,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-11T04:35:22.452Z"}},{"type":"Public","name":"STRetch","owner":"Oshlack","isFork":false,"description":"Method for detecting STR expansions from short-read sequencing data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":9,"starsCount":61,"forksCount":16,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-12-15T17:45:41.460Z"}},{"type":"Public","name":"MINTIE-paper-analysis","owner":"Oshlack","isFork":false,"description":"Code for generating the figures and analyses presented in the MINTIE paper","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-10-07T00:54:04.599Z"}},{"type":"Public","name":"Lace","owner":"Oshlack","isFork":false,"description":"Building SuperTranscripts: A linear representation of transcriptome data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":67,"forksCount":19,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-03-22T20:35:54.823Z"}},{"type":"Public","name":"AllSorts_v1","owner":"Oshlack","isFork":false,"description":"An Acute Lymphoblasitc Leukemia B-Cell classifier","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-01-18T03:35:06.812Z"}},{"type":"Public","name":"ec-dtu-pipe","owner":"Oshlack","isFork":false,"description":"Pipeline for performing differential transcript usage analysis using equivalence classes, transcript quantifications and/or exon counts","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-20T01:16:17.062Z"}},{"type":"Public","name":"necklace","owner":"Oshlack","isFork":false,"description":"Combine reference and assembled transcriptomes for RNA-Seq analysis","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":6,"starsCount":21,"forksCount":5,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-02-12T01:44:44.511Z"}},{"type":"Public","name":"ec-dtu-paper","owner":"Oshlack","isFork":false,"description":"Fast and accurate differential transcript usage by testing equivalence class counts","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-12-20T01:06:01.502Z"}},{"type":"Public","name":"ALL-RNAseq-utility-paper","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-08-05T01:28:41.931Z"}},{"type":"Public","name":"pooled-parents-paper","owner":"Oshlack","isFork":false,"description":"Code and analysis for the pooled parents paper","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-04-07T06:35:48.056Z"}},{"type":"Public","name":"combes-organoid-paper","owner":"Oshlack","isFork":false,"description":"Analysis code and output for the Combes kidney organoid scRNA-seq paper https://doi.org/10.1186/s13073-019-0615-0","allTopics":["rna-seq","kidney","single-cell","analysis","kidney-organoids"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":7,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-02-08T04:18:11.664Z"}},{"type":"Public","name":"OrganoidVarAnalysis","owner":"Oshlack","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-10-12T03:50:57.478Z"}}],"repositoryCount":38,"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":"Oshlack repositories"}