{"id":26022775,"url":"https://github.com/keniajin/protgear","last_synced_at":"2025-03-06T10:26:25.577Z","repository":{"id":151776365,"uuid":"320553265","full_name":"Keniajin/protGear","owner":"Keniajin","description":"protGear is a package for protein microarray data processing just before the main analysis.","archived":false,"fork":false,"pushed_at":"2023-02-03T19:25:58.000Z","size":43906,"stargazers_count":1,"open_issues_count":4,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-04-26T20:49:39.796Z","etag":null,"topics":["background-correction","microarray-data","normalisation","proteomics-data","r","shiny","shinydashboard"],"latest_commit_sha":null,"homepage":"https://keniajin.github.io/protGear/","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/Keniajin.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":"2020-12-11T11:20:58.000Z","updated_at":"2024-01-12T18:16:52.000Z","dependencies_parsed_at":null,"dependency_job_id":"f03be94c-306a-4f6b-a780-331d5edb4f2a","html_url":"https://github.com/Keniajin/protGear","commit_stats":{"total_commits":145,"total_committers":5,"mean_commits":29.0,"dds":0.1103448275862069,"last_synced_commit":"ff531ac35247c7d10264dcb2caa80126486f6723"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Keniajin%2FprotGear","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Keniajin%2FprotGear/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Keniajin%2FprotGear/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Keniajin%2FprotGear/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Keniajin","download_url":"https://codeload.github.com/Keniajin/protGear/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242128325,"owners_count":20076177,"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":["background-correction","microarray-data","normalisation","proteomics-data","r","shiny","shinydashboard"],"created_at":"2025-03-06T10:26:25.001Z","updated_at":"2025-03-06T10:26:25.562Z","avatar_url":"https://github.com/Keniajin.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"## General information\nprotGear is a package for protein micro-array data processing just before the main analysis. \n\nThe package loads the '`gpr`' or '`txt`' file format extracted by the quantification software and merges this with the specific sample identifiers. The package processes multiple files extracted in a batch with their corresponding sample identifier file. The sample identifier file has 2 variables '`v1`' and '`v2`' which indicate the mini-array or block number and sample identifier respectively. The '`gpr`' file and the corresponding sample identifier file have the same file name.  protGear also provides a web based $Shiny^{(R)}$ platform for real time visualization of the data processing. \n\nThere is a package vignette included with this package with a step by step use of the package. Check https://keniajin.github.io/protGear/ under articles. \n\n## Installing the devel package\n\n``` r\nlibrary(remotes) \nremotes::install_github(\"keniajin/protGear\")\n```\n\n\n## Installing from Bioc BioConductor\n\n``` r\n## install from BioConductor\nif (!require(\"BiocManager\", quietly = TRUE)) {\n  install.packages(\"BiocManager\")\n}\nBiocManager::install(\"protGear\")\n```\n\n## To run the shiny application\nTo use the application locally on your compute install R and launch the app using the following command. \n`protGear::launch_protGear_interactive()`\n\nTo Install R: \n - Open an Internet browser and go to www.r-project.org. \n - Under \"Getting Started\" click the \"download R\" link\n - Select a CRAN location (a mirror site) and click the corresponding link.\n - Download R depending on your operating system. \n\n## protGear help pages\n\n- The main page - https://keniajin.github.io/protGear/ \n- Vignette - https://keniajin.github.io/protGear/articles/vignette.html\n\n## Contribute\n\nCheck the Github page for [source \ncode](https://github.com/Keniajin/protGear/).\n\n\n## Publication \n\nMwai K, Kibinge N, Tuju J, Kamuyu G, Kimathi R, Mburu J, Chepsat E, Nyamako L, Chege T, Nkumama I, Kinyanjui S. et al. , protGear: A protein microarray data pre-processing suite. Computational and Structural Biotechnology Journal. 2021 Apr 24.\n\nDOI: https://doi.org/10.1016/j.csbj.2021.04.044 \n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeniajin%2Fprotgear","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkeniajin%2Fprotgear","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeniajin%2Fprotgear/lists"}