{"id":43932728,"url":"https://github.com/bionf/phyloprofiledata","last_synced_at":"2026-02-07T00:18:52.916Z","repository":{"id":114518778,"uuid":"189479106","full_name":"BIONF/PhyloProfileData","owner":"BIONF","description":"The PhyloProfileData package provides a collection of datasets to accompany the PhyloProfile package","archived":false,"fork":false,"pushed_at":"2025-06-25T07:18:01.000Z","size":29,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"devel","last_synced_at":"2025-09-09T16:36:12.981Z","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/BIONF.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS","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":"2019-05-30T20:36:36.000Z","updated_at":"2025-06-25T07:18:05.000Z","dependencies_parsed_at":"2025-09-10T06:31:40.059Z","dependency_job_id":null,"html_url":"https://github.com/BIONF/PhyloProfileData","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/BIONF/PhyloProfileData","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIONF%2FPhyloProfileData","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIONF%2FPhyloProfileData/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIONF%2FPhyloProfileData/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIONF%2FPhyloProfileData/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BIONF","download_url":"https://codeload.github.com/BIONF/PhyloProfileData/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIONF%2FPhyloProfileData/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29181312,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-06T23:15:33.022Z","status":"ssl_error","status_checked_at":"2026-02-06T23:15:09.128Z","response_time":59,"last_error":"SSL_read: 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":"2026-02-07T00:18:52.045Z","updated_at":"2026-02-07T00:18:52.885Z","avatar_url":"https://github.com/BIONF.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PhyloProfileData\n[![Bioconductor](https://img.shields.io/badge/available%20at-Bioconductor-orange)](https://bioconductor.org/packages/PhyloProfileData)\n\u003ca href=\"http://bioconductor.org/checkResults/release/data-experiment-LATEST/PhyloProfileData/\"\u003e\u003cimg border=\"0\" src=\"http://www.bioconductor.org/shields/build/release/data-experiment/PhyloProfileData.svg\" title=\"build results; click for full report\"\u003e\u003c/a\u003e.\n[![license: MIT](https://img.shields.io/badge/license-MIT-lightgrey.svg)](https://opensource.org/licenses/MIT)\n\n\nThe PhyloProfileData package provides a collection of datasets to accompany the \nR package [PhyloProfile pakage](https://github.com/BIONF/PhyloProfile) \n([Tran et al. 2018](https://doi.org/10.1093/bioinformatics/bty225)), where they \nare used to illustrate how to run PhyloProfile and analyse its results. Briefly,\nit contains the phylogenetic profiles, the fasta sequences and the domain \nannotations for two experimental data sets, including\n1. 147 human proteins in the AMPK-TOR pathway across 83 species, and\n2. 1011 BUSCO arthropoda ortholog groups across 88 species in the three domains \nof life.\n\n# Installation\n\n```r\nif (!requireNamespace(\"BiocManager\"))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"PhyloProfileData\")\n```\n\n# Usage\n\nThe data are stored in the \n[ExperimentHub](https://bioconductor.org/packages/release/bioc/html/ExperimentHub.html) \nof [Bioconductor](http://bioconductor.org) and can be accessed using the \nfollowing R commands:\n\n```r\n# Load the data of the PhyloProfileData package\nlibrary(ExperimentHub)\neh = ExperimentHub()\nmyData \u003c- query(eh, \"PhyloProfileData\")\n# View the metadata of this data package\nmyData\n```\n\n```\nExperimentHub with 6 records\n# snapshotDate(): 2019-05-29 \n# $dataprovider: Applied Bioinformatics Dept., Goethe University Frankfurt\n# $species: NA\n# $rdataclass: data.frame, AAStringSet\n# additional mcols(): taxonomyid, genome, description, coordinate_1_based,\n#   maintainer, rdatadateadded, preparerclass, tags, rdatapath, sourceurl,\n#   sourcetype \n# retrieve records with, e.g., 'object[[\"EH2544\"]]' \n\n           title                                                                         \n  EH2544 | Phylogenetic profiles of human AMPK-TOR pathway                               \n  EH2545 | FASTA sequences for proteins in the phylogenetic profiles of human AMPK-TOR...\n  EH2546 | Domain annotations for proteins in the phylogenetic profiles of human AMPK-...\n  EH2547 | Phylogenetic profiles of BUSCO arthropoda proteins                            \n  EH2548 | FASTA sequences for proteins in the phylogenetic profiles of BUSCO arthropo...\n  EH2549 | Domain annotations for proteins in the phylogenetic profiles of BUSCO arthr...\n```\n\n\nEach data set contains three files (objects) corresponding for the phylogenetic \nprofiles, the FASTA sequences and the protein domain annotations. A particular \ndata object can be retrieve using its ID, for example:\n\n```r\n# Retrieve FASTA sequences for proteins in the phylogenetic profiles of the \n# human AMPK-TOR pathway\nampkTorFasta \u003c- myData[[\"EH2545\"]]\n```\n\nFor a detailed description of each data set and the belonging data objects \nplease see the vignette PhyloProfileData.\n\n```r\nlibrary(PhyloProfileData)\nbrowseVignettes(\"PhyloProfileData\")\n```\n\n# Bugs, Comments and Suggests\nAny bug reports or comments, suggestionsare highly appreciated. Please [open an \nissue on GitHub](https://github.com/BIONF/PhyloProfileData/issues/new) or be in \ntouch [via email](mailto:tran@bio.uni-frankfurt.de).\n\n# Contributors\n* [Vinh](https://github.com/trvinh)\n* [Hannah](https://github.com/mueli94)\n\n# License\nThis data package is released under [MIT license](https://github.com/BIONF/PhyloProfile/blob/master/LICENSE).\n\n# How-To Cite\nNgoc-Vinh Tran, Bastian Greshake Tzovaras, Ingo Ebersberger; PhyloProfile: Dynamic visualization and exploration of multi-layered phylogenetic profiles, Bioinformatics, , bty225, https://doi.org/10.1093/bioinformatics/bty225\n\nor use the citation function in R CMD to have it directly in BibTex or LaTeX format\n```r\ncitation(\"PhyloProfileData\")\n```\n\n# Contact\nVinh Tran\ntran@bio.uni-frankfurt.de\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionf%2Fphyloprofiledata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbionf%2Fphyloprofiledata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionf%2Fphyloprofiledata/lists"}