{"id":22092151,"url":"https://github.com/pcruniversum/rdml","last_synced_at":"2025-07-24T20:32:03.612Z","repository":{"id":20418465,"uuid":"23694860","full_name":"PCRuniversum/RDML","owner":"PCRuniversum","description":"RDML data import for R","archived":false,"fork":false,"pushed_at":"2022-10-18T12:06:54.000Z","size":13512,"stargazers_count":20,"open_issues_count":4,"forks_count":7,"subscribers_count":7,"default_branch":"master","last_synced_at":"2023-11-20T15:09:31.236Z","etag":null,"topics":["bioinformatics","cran","pcr","qpcr","r","rdml"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PCRuniversum.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-09-05T07:52:50.000Z","updated_at":"2023-03-13T18:44:10.000Z","dependencies_parsed_at":"2022-07-26T06:46:55.000Z","dependency_job_id":null,"html_url":"https://github.com/PCRuniversum/RDML","commit_stats":null,"previous_names":["kablag/rdml"],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FRDML","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FRDML/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FRDML/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PCRuniversum%2FRDML/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PCRuniversum","download_url":"https://codeload.github.com/PCRuniversum/RDML/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":227476143,"owners_count":17779417,"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":["bioinformatics","cran","pcr","qpcr","r","rdml"],"created_at":"2024-12-01T03:08:27.588Z","updated_at":"2024-12-01T03:08:28.292Z","avatar_url":"https://github.com/PCRuniversum.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![published in: Bioinformatics](https://img.shields.io/badge/published%20in-Bioinformatics-ff69b4.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btx528)\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/RDML)](https://CRAN.R-project.org/package=RDML)\n[![Downloads](https://cranlogs.r-pkg.org/badges/RDML)]( https://CRAN.R-project.org/package=RDML)\n[![Travis-CI Build Status](https://travis-ci.org/pcruniversum/RDML.svg?branch=master)](https://travis-ci.org/pcruniversum/RDML)\n[![Rdoc](http://www.rdocumentation.org/badges/version/RDML)](http://www.rdocumentation.org/packages/RDML) \n\n\u003cimg src=\"https://raw.githubusercontent.com/pcruniversum/RDML/master/vignettes/RDML_logo.png\" alt=\"RDML\" width=\"100%\"\u003e\n\nThe RDML package is published in Oxford Bioinformatics: \nStefan Rödiger, Michał Burdukiewicz, Andrej-Nikolai Spiess, Konstantin Blagodatskikh; Enabling reproducible real-time quantitative PCR research: the RDML package, Bioinformatics, [https://doi.org/10.1093/bioinformatics/btx528](https://doi.org/10.1093/bioinformatics/btx528) (see also `citation()`).\n\nImports qPCR data from RDML v1.1 format files ([Lefever et al. 2009](http://nar.oxfordjournals.org/content/32/5/1792.abstract?view=long\u0026pmid=19223324)) and \ntransforms it to the appropriate format of the qpcR package (Ritz et al. 2008, \nSpiess et al. 2008) or chipPCR package. [RDML](http://www.rdml.org/) (Real-time PCR Data Markup \nLanguage) is the recommended file format element in the Minimum Information for \nPublication of Quantitative Real-Time PCR Experiments (MIQE) guidelines ([Bustin et al. 2009](http://clinchem.aaccjnls.org/content/55/4/611.long)).\n\n# Installation\n------------\n\nThe stable version of the `RDML` package for R is hosted on [CRAN](https://CRAN.R-project.org/package=RDML) and can be installed as any R package.\n\nYou can install the latest development version of the code using the `devtools` R package.\n\n```r\n# Install devtools, if you haven't already.\ninstall.packages(\"devtools\")\n\nlibrary(devtools)\ninstall_github(\"PCRuniversum/RDML\")\n```\n\n# Manual\n\nThe manual is available [online](https://pcruniversum.github.io/RDML/).\n\n# Examples\n\n`RDML` imports various data formats (CSV, XMLX) besides the RDML format. Provided that the raw data \nhave a defined structure (as described in the vignette) the import should be \ndone by a few clicks. The example below shows the import of amplification curve\ndata, which were stored in a CSV file. The function `rdmlEdit()` was used in the \n[RKWard IDE/GUI](https://rkward.kde.org/) for further processing. rdmlEdit may be also accessed as a web server (http://shtest.evrogen.net/rdmlEdit/). \n\n\u003cimg src=\"https://raw.githubusercontent.com/pcruniversum/RDML/master/vignettes/File_import.png\" alt=\"Data Import\" width=\"100%\"\u003e\n\nOnce imported enables `rdmlEdit()` and other functions from the `RDML` package complex \ndata visualization and processing in the R statistical computing environment.\n\n\u003cimg src=\"https://raw.githubusercontent.com/pcruniversum/RDML/master/vignettes/data_view.png\" alt=\"Data View\" width=\"100%\"\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpcruniversum%2Frdml","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpcruniversum%2Frdml","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpcruniversum%2Frdml/lists"}