{"id":19624254,"url":"https://github.com/bioconductor/hcabrowser","last_synced_at":"2025-04-28T05:31:30.369Z","repository":{"id":146388464,"uuid":"133706475","full_name":"Bioconductor/HCABrowser","owner":"Bioconductor","description":"Browse the Human Cell Atlas data portal","archived":false,"fork":false,"pushed_at":"2023-03-10T18:15:34.000Z","size":528,"stargazers_count":8,"open_issues_count":0,"forks_count":4,"subscribers_count":11,"default_branch":"devel","last_synced_at":"2024-05-09T07:47:28.503Z","etag":null,"topics":["bioconductor","human-cell-atlas"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-05-16T18:15:14.000Z","updated_at":"2023-03-10T18:15:39.000Z","dependencies_parsed_at":"2023-10-20T18:25:45.029Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/HCABrowser","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/Bioconductor%2FHCABrowser","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FHCABrowser/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FHCABrowser/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FHCABrowser/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/HCABrowser/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224096930,"owners_count":17255192,"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":["bioconductor","human-cell-atlas"],"created_at":"2024-11-11T11:37:26.097Z","updated_at":"2024-11-11T11:37:27.647Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\nThe Human Cell Atlas (https://www.humancellatlas.org/) was created in\norder to create comprehensive reference maps of all human cells as a basis for\nboth understanding human health and diagnosing, monitoring, and treating\ndisease. The *HCABrowser* Biocondctor pacakge provides infrastructure for\nsearching for, queerying, and accessing data help on the Human Cell Atlas's\nData Coordination Platform (https://dss.data.humancellatlas.org/). Further\nchanges to the package are planned to incorperate higer level functionality to\nupload user generated data to the the Human Cell Atlas platform.\n\nThis is a Biocondcutor package and can be installed using `BiocManager`.\n```\n## Install Bioconductor\nif (!requireNamespace(\"BiocManager\"))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"HCABrowser\")\n\nlibrary(HCABrowser)\n```\n\nThis package introduces the `HCABrowser` object used to connect to and\nperform opertions on the Human Cell Atlas\n```\nhca \u003c- HCABrowser()\nhca\n```\n\nThe Human Cell Atlas Data Portal requires queries to be submitted against\ntheir schema. Given the schema is complicated and users may not want to\nlearn it in order to search the Human Cell Atlas, we seek to offer an easier\nway for the user to explore the Human Cell Atlas.\n\nFirst we want to see which fields and values of fields are available.\n```\n## Show fields and their respective abbreviations\nhca %\u003e% fields\n\n## Show availiable values for a field (e.g. organ.text)\nhca %\u003e% values(organ.text)\n\n## OR show all values for all fields\nhca %\u003e% values\n```\n\nThe `filter()` and `select()` methods are used to query the Human Cell Atlas.\n\n```\n## Search for bundles regarding blood and that were no constructed with Smart-Seq2\nhca \u003c- hca %\u003e% filter(organ.text == \"blood\" \u0026\u0026 library_construction_approach.text != \"Smart-Seq2\")\nhca\n\n## Include columns for 'project_title' and 'project_shortname'\nhca \u003c- hca %\u003e% select(c('project_title', 'project_shortname'))\nhca\n```\n\nOnce the data bundles of interest are found, they can be downloaded and used to\nobtain data. We then use these bundles to download the expression matrices using\nthe HCAMatrixBrowser package.\n```\nbundles \u003c- hca %\u003e% pullBundles\n\nif (!requireNamespace(\"HCAMatrixBrowser\"))\n    BiocManager::install(\"HCAMatrixBrowser\")\n\nlibrary(HCAMatrixBrowser)\n\nloadHCAMatrix(bundles)\n```\n\nFor my information, please refer to the package's vignette.\n\nAs with other Biocondcutor packages, the `master` branch indicates the\ndevelopment branch and the `RELEASE_X_X` branch indicates the current\nrelease branch.\n\n- API: https://dss.data.humancellatlas.org/\n- schema https://github.com/HumanCellAtlas/metadata-schema\n- typical tasks: https://github.com/HumanCellAtlas/data-consumer-vignettes\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fhcabrowser","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fhcabrowser","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fhcabrowser/lists"}