https://github.com/pcruniversum/rdml

RDML data import for R
https://github.com/pcruniversum/rdml

bioinformatics cran pcr qpcr r rdml

Last synced: 3 months ago
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RDML data import for R

• Host: GitHub
• URL: https://github.com/pcruniversum/rdml
• Owner: PCRuniversum
• License: other
• Created: 2014-09-05T07:52:50.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2022-10-18T12:06:54.000Z (over 2 years ago)
• Last Synced: 2023-11-20T15:09:31.236Z (over 1 year ago)
• Topics: bioinformatics, cran, pcr, qpcr, r, rdml
• Language: R
• Homepage:
• Size: 12.9 MB
• Stars: 20
• Watchers: 7
• Forks: 7
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG
  • License: LICENSE

Awesome Lists containing this project

README

        
[![published in: Bioinformatics](https://img.shields.io/badge/published%20in-Bioinformatics-ff69b4.svg?style=flat)](https://doi.org/10.1093/bioinformatics/btx528)

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/RDML)](https://CRAN.R-project.org/package=RDML)

[![Downloads](https://cranlogs.r-pkg.org/badges/RDML)]( https://CRAN.R-project.org/package=RDML)

[![Travis-CI Build Status](https://travis-ci.org/pcruniversum/RDML.svg?branch=master)](https://travis-ci.org/pcruniversum/RDML)

[![Rdoc](http://www.rdocumentation.org/badges/version/RDML)](http://www.rdocumentation.org/packages/RDML) 



The RDML package is published in Oxford Bioinformatics: 

Stefan 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()`).

Imports qPCR data from RDML v1.1 format files ([Lefever et al. 2009](http://nar.oxfordjournals.org/content/32/5/1792.abstract?view=long&pmid=19223324)) and 

transforms it to the appropriate format of the qpcR package (Ritz et al. 2008, 

Spiess et al. 2008) or chipPCR package. [RDML](http://www.rdml.org/) (Real-time PCR Data Markup 

Language) is the recommended file format element in the Minimum Information for 

Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines ([Bustin et al. 2009](http://clinchem.aaccjnls.org/content/55/4/611.long)).

# Installation

------------

The 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.

You can install the latest development version of the code using the `devtools` R package.

```r

# Install devtools, if you haven't already.

install.packages("devtools")

library(devtools)

install_github("PCRuniversum/RDML")

```

# Manual

The manual is available [online](https://pcruniversum.github.io/RDML/).

# Examples

`RDML` imports various data formats (CSV, XMLX) besides the RDML format. Provided that the raw data 

have a defined structure (as described in the vignette) the import should be 

done by a few clicks. The example below shows the import of amplification curve

data, which were stored in a CSV file. The function `rdmlEdit()` was used in the 

[RKWard IDE/GUI](https://rkward.kde.org/) for further processing. rdmlEdit may be also accessed as a web server (http://shtest.evrogen.net/rdmlEdit/). 



Once imported enables `rdmlEdit()` and other functions from the `RDML` package complex 

data visualization and processing in the R statistical computing environment.