{"id":23046196,"url":"https://github.com/cpanse/tartare","last_synced_at":"2025-04-03T02:20:43.920Z","repository":{"id":88060434,"uuid":"198232427","full_name":"cpanse/tartare","owner":"cpanse","description":"raw file collection recorded on Thermo Fisher Scientific mass spectrometers for extented unit testing","archived":false,"fork":false,"pushed_at":"2019-10-28T14:31:19.000Z","size":65,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-08T16:28:45.422Z","etag":null,"topics":["bioconductor","blob","data","r","unittesting"],"latest_commit_sha":null,"homepage":"https://bioconductor.org/packages/devel/data/experiment/html/tartare.html","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/cpanse.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-07-22T13:48:51.000Z","updated_at":"2024-02-24T20:14:22.000Z","dependencies_parsed_at":"2023-03-02T01:00:18.176Z","dependency_job_id":null,"html_url":"https://github.com/cpanse/tartare","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/cpanse%2Ftartare","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2Ftartare/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2Ftartare/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cpanse%2Ftartare/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cpanse","download_url":"https://codeload.github.com/cpanse/tartare/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246922661,"owners_count":20855430,"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","blob","data","r","unittesting"],"created_at":"2024-12-15T21:30:51.888Z","updated_at":"2025-04-03T02:20:43.897Z","avatar_url":"https://github.com/cpanse.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# tartare\n\nraw file collection recorded on Thermo Fisher Scientific mass spectrometers for\nextented unit testing\n\nhttps://github.com/Bioconductor/Contributions/issues/1286\n\n## install \n\n```\n# Release (3.10) \nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"tartare\", version=\"devel\")\n```\n\nsee also https://bioconductor.org/packages/tartare/\n\n## requires\n\nthe following usage example requires the following packages:\n\n1. https://github.com/rformassspectrometry/Spectra\n2. https://github.com/cpanse/MsBackendRawFileReader\n\n\n![schema](https://raw.githubusercontent.com/jorainer/swemsa_2019/master/images/Spectra-backends-02.png)\nCourtesy of [@jorainer](https://github.com/jorainer); SWEMSA 2019 conference in Erding, Germany [10.5281/zenodo.3499649](https://doi.org/10.5281/zenodo.3499649).\n\n\n\n\n## usage\n\ntaken from the help pages `?tartare`.\n\n```\nlibrary(tartare)\nlibrary(ExperimentHub)\n\neh \u003c- ExperimentHub()\n(files \u003c- getFilename(eh))\n\nlibrary(MsBackendRawFileReader)\n\nbe \u003c- lapply(files, function(f){\nif (grepl(\"mzXML$\", f))\n    backendInitialize(MsBackendMzR(), files = f)\nelse\n    backendInitialize(MsBackendRawFileReader(), files = f, extra=FALSE)\n})\n\nbe\n```\n\n```\nR\u003e be\n$EH3219\nMsBackendMzR with 1764 spectra\n       msLevel     rtime scanIndex\n     \u003cinteger\u003e \u003cnumeric\u003e \u003cinteger\u003e\n1            1  0.215344         1\n2            1  0.713714         2\n3            1   1.10822         3\n4            1   1.50284         4\n5            1   1.89709         5\n...        ...       ...       ...\n1760         2   239.767      1760\n1761         2   239.834      1761\n1762         2   239.901      1762\n1763         2   239.969      1763\n1764         2   240.036      1764\n ... 31 more variables/columns.\n\nfile(s):\n203c4d41aa69_3235\n\n$EH3220\n\nfilename:\t/Users/cp/Library/Caches/ExperimentHub/203c576b7cbf_3236.raw\ncreation date:\t7/11/2019 11:04:01 AM\nfirst scan:\t1\nlast scan:\t1877\nmodel:\tQ Exactive HF-X Orbitrap\nname:\tQ Exactive HF-X Orbitrap\nSerialNumber:\tExactive Series slot #6114 \n\n\n$EH3221\nMsBackendMzR with 8742 spectra\n       msLevel     rtime scanIndex\n     \u003cinteger\u003e \u003cnumeric\u003e \u003cinteger\u003e\n1            1 0.0653085         1\n2            1  0.392698         2\n3            1  0.720055         3\n4            1   1.04732         4\n5            1   1.37468         5\n...        ...       ...       ...\n8738         1   2099.13      8738\n8739         1   2099.44      8739\n8740         1   2099.76      8740\n8741         1   2100.07      8741\n8742         1   2100.38      8742\n ... 31 more variables/columns.\n\nfile(s):\n203c51cb0c6f_3237\n\n$EH3222\n\nfilename:\t/Users/cp/Library/Caches/ExperimentHub/24ab678291f6_3238.raw\ncreation date:\t7/16/2019 5:56:24 PM\nfirst scan:\t1\nlast scan:\t8742\nmodel:\tOrbitrap Fusion Lumos\nname:\tOrbitrap Fusion Lumos\nSerialNumber:\tFSN20583 \n\n\nR\u003e \n```\n\n```\nhfx.filename \u003c- getFilename(eh, c('tartar', '20190710_003_PierceHeLaProteinDigestStd.raw'));\nx \u003c- .cnew (\"Rawfile\", hfx.filename);\nx$GetInfoValues()\n```\n\n```\nsee ?tartare and browseVignettes('tartare') for documentation\ndownloading 0 resources\nloading from cache\n[1] \"/Users/cp/Library/Caches/ExperimentHub/203c576b7cbf_3236.raw\"\n[2] \"7/11/2019 11:04:01 AM\"                                       \n[3] \"1\"                                                           \n[4] \"1877\"                                                        \n[5] \"Q Exactive HF-X Orbitrap\"                                    \n[6] \"Q Exactive HF-X Orbitrap\"                                    \n[7] \"Exactive Series slot #6114\"       \n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcpanse%2Ftartare","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcpanse%2Ftartare","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcpanse%2Ftartare/lists"}