{"id":22580184,"url":"https://github.com/vccri/ularcirc","last_synced_at":"2025-04-10T18:31:38.900Z","repository":{"id":47698887,"uuid":"126766911","full_name":"VCCRI/Ularcirc","owner":"VCCRI","description":"An R-shiny app that provides backsplice and canonical splicing analysis for both circular RNA (circRNA) and parental transcripts","archived":false,"fork":false,"pushed_at":"2022-04-06T11:43:19.000Z","size":57183,"stargazers_count":15,"open_issues_count":7,"forks_count":7,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-24T16:11:05.406Z","etag":null,"topics":["backsplicing","circrna","circular-rna","rna-seq","rna-seq-analysis","sequencing-rna","splicing-analyses","splicing-visualization"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/VCCRI.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-03-26T03:11:51.000Z","updated_at":"2023-10-28T12:21:09.000Z","dependencies_parsed_at":"2022-08-17T15:25:38.389Z","dependency_job_id":null,"html_url":"https://github.com/VCCRI/Ularcirc","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VCCRI%2FUlarcirc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VCCRI%2FUlarcirc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VCCRI%2FUlarcirc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/VCCRI%2FUlarcirc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/VCCRI","download_url":"https://codeload.github.com/VCCRI/Ularcirc/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248271546,"owners_count":21075800,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["backsplicing","circrna","circular-rna","rna-seq","rna-seq-analysis","sequencing-rna","splicing-analyses","splicing-visualization"],"created_at":"2024-12-08T05:14:24.937Z","updated_at":"2025-04-10T18:31:38.864Z","avatar_url":"https://github.com/VCCRI.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Ularcirc\nAn R package that provides analysis and visualisation of canonical and backsplice junctions.\nTakes output provided by the STAR aligner as well as CIRI2 and circExplorer2 output and enables circRNA downstream analysis.\n\nAuthor and maintainer: David Humphreys (d.humphreys  at      victorchang  dot   edu   dot    au)\n\nUlarcirc manuscript now available through [Nucleic Acids Research](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz718/5552786). \n\n# Installation\nYou can install Ularcirc using the 'devtools' package.  \n\n    \u003e install.packages(\"devtools\")\n    \u003e library(devtools)\n    \u003e devtools::install_github(\"VCCRI/Ularcirc\", build = TRUE, build_vignettes = TRUE, build_opts = c(\"--no-resave-data\", \"--no-manual\"))\n\nUlarcirc can annotate circRNA with overlapping gene information. This is obtained from available \nbioconductor databases. Use the following command to identify what databases to download:\n\n    \u003e library(\"Ularcirc\")\n    \u003e all_dbs \u003c- Compatible_Annotation_DBs() # This will return all compatible databases\n    \u003e mmu_dbs \u003c- Compatible_Annotation_DBs(search_term = 'mm10') # returns mm10 compatible databases\n    \u003e # Lets see what is stored in mmu_dbs\n    \u003e mmu_dbs\n   annotation     genome                         txdb                                \n16 \"org.Mm.eg.db\" \"BSgenome.Mmusculus.UCSC.mm10\" \"TxDb.Mmusculus.UCSC.mm10.ensGene\"  \n17 \"org.Mm.eg.db\" \"BSgenome.Mmusculus.UCSC.mm10\" \"TxDb.Mmusculus.UCSC.mm10.knownGene\"\n    \n    \u003e # Now lets download all of the above databases\n    \u003e if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")   # Make sure R is looking at bioconductor repository\n    \u003e BiocManager::install(c(mmu_dbs))\n    \n    \nTo start Ularcirc shiny app\n\n    \u003e library('Ularcirc')\n\t  \u003e Ularcirc()\n\n\t\n# Documentation\nPlease refer to vignette within R. Additionally  there are a number of screen casts that highlights how to get going with Ularcirc.\n\n##Screen casts\n\nPlease click [this link to view a ~5 minute screen cast](https://youtu.be/96rcxlh_aLA) that walks through a simple circRNA analysis using Ularcirc.\n\nThe following link demonstrates how to [upload and recover sequence information from BSJ and FSJ](https://youtu.be/txWAI-LJCVw)\n\n\n##  Features\n\n* Friendly user interface\n* Circular RNA detection independent of gene annotation.\n* Provides visualisation of forward AND backsplice junctions\n* Recover predicted circRNA sequence\n* Recover sequence of backsplice junctions and forward splice junctions\n* Support both single-read and paired-end sequencing (paired end prefered).\n* Detect miRNA binding sites\n* detect putative open reading frame of circRNA\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvccri%2Fularcirc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvccri%2Fularcirc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvccri%2Fularcirc/lists"}