{"id":49687056,"url":"https://github.com/csiro/epitranscriptome","last_synced_at":"2026-05-07T10:41:19.930Z","repository":{"id":354929597,"uuid":"1025394885","full_name":"csiro/epitranscriptome","owner":"csiro","description":null,"archived":false,"fork":false,"pushed_at":"2026-05-01T00:03:49.000Z","size":119,"stargazers_count":0,"open_issues_count":3,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2026-05-01T02:08:12.901Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/csiro.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-07-24T07:33:05.000Z","updated_at":"2026-05-01T00:03:55.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/csiro/epitranscriptome","commit_stats":null,"previous_names":["csiro/epitranscriptome"],"tags_count":null,"template":false,"template_full_name":null,"purl":"pkg:github/csiro/epitranscriptome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Fepitranscriptome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Fepitranscriptome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Fepitranscriptome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Fepitranscriptome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/csiro","download_url":"https://codeload.github.com/csiro/epitranscriptome/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/csiro%2Fepitranscriptome/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32734383,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-07T02:14:30.463Z","status":"ssl_error","status_checked_at":"2026-05-07T02:14:29.405Z","response_time":62,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":[],"created_at":"2026-05-07T10:41:18.509Z","updated_at":"2026-05-07T10:41:19.920Z","avatar_url":"https://github.com/csiro.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Epitranscriptome Explorer\n\nA shiny app for the exploration of RNA epitranscriptomic data (polyadenylation\nand m6A/m5C methylation). For now, the input data for this app must be preprocessed \nthrough the accompanying `preprocess_polya_methyl.R` script. \nThis script combines two (or more) sample runs into RDS files representing \nmerged and filtered data.tables, one for PolyA length and one for m6A/m5C methylation.\nThe app acts independently on PolyA and methylation data, although in most cases \nwe would be comparing data from the same sample runs.\n\nThe starting point for the app are the two upload buttons for PolyA and methylation\nRDS files. These upload client side RDS files to a temp location on the server. \nThe app may be set to pre-load existing files on the server side through the \n`config.json` configuration file. Note that if the shiny server is running locally,\n`config.json` may point to local files, however if the server is remote, the only\nway shiny can access local user files is through the upload buttons. The max upload\nsize is set fairly large, but it may be possible that some files are just too \nlarge (the app tends to start to struggle with two \u003e500MB RDSs).\n\nThe filter section subsets the data by transcript type (eg. protein coding, rRNA,\nunprocessed pseudogene), particular genes (a simple comma separated list of gene\nnames may be uploaded) or particular transcripts. The transcript filter only becomes\nactive when the data has already been filtered down to a few genes. For these\ninput selectors, empty or blank should be interpreted as \"no filter\"/everything.\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsiro%2Fepitranscriptome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcsiro%2Fepitranscriptome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcsiro%2Fepitranscriptome/lists"}