{"id":16698394,"url":"https://github.com/lgatto/proteomicsannotationhubdata","last_synced_at":"2025-03-14T04:09:10.408Z","repository":{"id":33934618,"uuid":"37658149","full_name":"lgatto/ProteomicsAnnotationHubData","owner":"lgatto","description":"Annotation hub data for proteomics data","archived":false,"fork":false,"pushed_at":"2022-01-06T11:46:42.000Z","size":109,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-01-20T23:12:50.246Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lgatto.png","metadata":{"files":{"readme":"README.Rmd","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}},"created_at":"2015-06-18T12:27:24.000Z","updated_at":"2022-01-06T11:46:46.000Z","dependencies_parsed_at":"2022-07-13T16:48:05.382Z","dependency_job_id":null,"html_url":"https://github.com/lgatto/ProteomicsAnnotationHubData","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/lgatto%2FProteomicsAnnotationHubData","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FProteomicsAnnotationHubData/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FProteomicsAnnotationHubData/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lgatto%2FProteomicsAnnotationHubData/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lgatto","download_url":"https://codeload.github.com/lgatto/ProteomicsAnnotationHubData/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243521281,"owners_count":20304186,"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":[],"created_at":"2024-10-12T17:51:54.750Z","updated_at":"2025-03-14T04:09:10.380Z","avatar_url":"https://github.com/lgatto.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# `AnnotationHub` for proteomics\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r env, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\nsuppressPackageStartupMessages(library(\"BiocStyle\"))\n```\n\nThe aim of this package is to offer access to mass spectrometry and\nproteomics data throught the `r Biocpkg(\"AnnotationHub\")`\ninfrastructure.\n\n\n\n```{r ahinit}\nlibrary(\"AnnotationHub\")\nah \u003c- AnnotationHub()\nah\n```\n\nLet's start by querying the entries that originate from the PRIDE\ndatabase:\n\n```{r provider}\nquery(ah, \"PRIDE\")\n```\n\nOr those of a specific project\n\n```{r title}\nah[grep(\"PXD000001\", ah$title)]\n```\n\nTo see the metadata of a specific entry, we use its AnnotationHub\nentry number inside single `[`\n\n```{r ah49008}\nah[\"AH49008\"]\n```\n\nTo access the actual data, raw mass spectrometry data in this case, we\ndouble the `[[`\n\n```{r rawmsdata}\nlibrary(\"mzR\")\nrw \u003c- ah[[\"AH49008\"]]\nrw\n```\n\nIn this case, we have an instance of class `r as.character(class(rw))`,\nthat can be processed as anticipated.\n\nIn the short demonstration above, we had **direct** and\n**standardised** access to the raw data, without a need to manually\nopen this raw data or worry about the file format. The data was\nprepared and converted into a **standard Bioconductor data types** for\nimmediate consumption by the user. This is also valid for other\nrelevant data types such as identification results, fasta files or\nprotein of peptide quantitation data.\n\nSee the `ProteomicsAnnotationHubData` vignette for details on\navailable data and how to add new proteomics data to AnnotationHub.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flgatto%2Fproteomicsannotationhubdata","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flgatto%2Fproteomicsannotationhubdata","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flgatto%2Fproteomicsannotationhubdata/lists"}