{"id":19624303,"url":"https://github.com/bioconductor/googlegenomics","last_synced_at":"2025-08-26T08:13:36.497Z","repository":{"id":16532427,"uuid":"19285708","full_name":"Bioconductor/GoogleGenomics","owner":"Bioconductor","description":"An R package for Google Genomics API queries.","archived":false,"fork":false,"pushed_at":"2023-03-15T20:25:05.000Z","size":388,"stargazers_count":42,"open_issues_count":8,"forks_count":26,"subscribers_count":40,"default_branch":"devel","last_synced_at":"2024-05-09T07:46:37.036Z","etag":null,"topics":["bioconductor-packages","core-package","retired-package"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":"CONTRIBUTING.rst","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2014-04-29T17:41:58.000Z","updated_at":"2024-05-01T15:53:11.000Z","dependencies_parsed_at":"2023-10-20T18:25:44.442Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/GoogleGenomics","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FGoogleGenomics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FGoogleGenomics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FGoogleGenomics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FGoogleGenomics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/GoogleGenomics/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224096987,"owners_count":17255200,"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-packages","core-package","retired-package"],"created_at":"2024-11-11T11:37:38.977Z","updated_at":"2024-11-11T11:37:39.711Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"GoogleGenomics  |Build Status|_\n===============================\n\n.. |Build Status| image:: http://img.shields.io/travis/Bioconductor/GoogleGenomics.svg?style=flat\n.. _Build Status: https://travis-ci.org/Bioconductor/GoogleGenomics\n\n.. role:: r(code)\n   :language: r\n\n.. role:: sh(code)\n   :language: sh\n\nThis R client fetches reads and variants data from the `Google Genomics API`_\nand provides converters to obtain `Bioconductor`_ S4 classes like GAlignments,\nand GRanges and VRanges.\n\n.. _Google Genomics API: https://cloud.google.com/genomics\n.. _Bioconductor: http://www.bioconductor.org/\n.. _gRPC: https://grpc.io/\n\nInstalling\n----------\n\nUse the Bioconductor repositories to install this package.\n\nIf you have `gRPC`_ installed, you will be able to access the entire v1\nGoogle Genomics API through the :r:`callGRPCMethod` function provided in\nthe package and use more performant reads and variant search methods.\nWithout gRPC support, you will still be able to query reads and variants;\nsee the vignettes for sample usage.\n\n* [Optional] Installing gRPC\n\n  See `our guide on gRPC \u003cGRPC.rst\u003e`_.\n\n* Installing R package\n\n  .. code:: r\n\n    source(\"http://bioconductor.org/biocLite.R\")\n    useDevel(TRUE) # Skip this step if you do not want the devel version.\n\n    biocLite(\"GoogleGenomics\")  # If gRPC is not installed.\n    biocLite(\"GoogleGenomics\", type=\"source\")  # If gRPC is installed.\n    library(GoogleGenomics)\n\nAuthentication\n--------------\n\nCall :r:`authenticate` to set up credentials. Check the function\ndocumentation for details on various available options. The function will\nreturn :r:`TRUE` on successful authentication.\n\nExamples\n--------\n\nSee the following examples for more detail:\n\n* `Working with Reads \u003chttp://bioconductor.org/packages/devel/bioc/vignettes/GoogleGenomics/inst/doc/PlottingAlignments.html\u003e`_\n\n* `Working with Variants \u003chttp://bioconductor.org/packages/devel/bioc/vignettes/GoogleGenomics/inst/doc/AnnotatingVariants.html\u003e`_\n\n* `Variant Annotation Comparison Test \u003chttp://bioconductor.org/packages/devel/bioc/vignettes/GoogleGenomics/inst/doc/VariantAnnotation-comparison-test.html\u003e`_\n\n* and also the `integration tests \u003c./tests/testthat\u003e`_\n\nProject status\n--------------\n\nThe package is integrated with gRPC when available on the system where the\npackage was built. With gRPC support, the entire v1 API is accessible.\nWithout gRPC support, this package can be used to search for reads and\nvariants, and convert them to various Bioconductor formats.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fgooglegenomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fgooglegenomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fgooglegenomics/lists"}