Data

Tools

Indexes

Applications

Experiments

Open Source Science

RDML

RDML data import for R

https://github.com/PCRuniversum/RDML

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

bioinformatics cran pcr qpcr r rdml
Last synced: 10 months ago · JSON representation

Repository

RDML data import for R

Basic Info
  • Host: GitHub
  • Owner: PCRuniversum
  • License: other
  • Language: HTML
  • Default Branch: master
  • Homepage:
  • Size: 13 MB
Statistics
  • Stars: 21
  • Watchers: 6
  • Forks: 8
  • Open Issues: 4
  • Releases: 0
Topics
bioinformatics cran pcr qpcr r rdml
Created almost 12 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License

README.md

published in: Bioinformatics CRAN_Status_Badge Downloads Travis-CI Build Status Rdoc

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 (see also citation()).

Imports qPCR data from RDML v1.1 format files (Lefever et al. 2009) and transforms it to the appropriate format of the qpcR package (Ritz et al. 2008, Spiess et al. 2008) or chipPCR package. RDML (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).

Installation

The stable version of the RDML package for R is hosted on CRAN 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.

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 for further processing. rdmlEdit may be also accessed as a web server (http://shtest.evrogen.net/rdmlEdit/).

Data Import

Once imported enables rdmlEdit() and other functions from the RDML package complex data visualization and processing in the R statistical computing environment.

Data View

Owner

  • Name: PCRuniversum
  • Login: PCRuniversum
  • Kind: organization

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 495
  • Total Committers: 7
  • Avg Commits per committer: 70.714
  • Development Distribution Score (DDS): 0.337
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
kablag k****g@y****u 328
michbur m****z@g****m 75
devSJR s****r@h****e 38
devSJR s****r@b****e 29
kablag k****g@g****m 22
devSJR d****R 2
Jakob Steiner j****r@h****m 1
Committer Domains (Top 20 + Academic)
b-tu.de: 1 hs-lausitz.de: 1 yandex.ru: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 33
  • Total pull requests: 2
  • Average time to close issues: 4 months
  • Average time to close pull requests: 25 minutes
  • Total issue authors: 12
  • Total pull request authors: 2
  • Average comments per issue: 1.36
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kablag (16)
  • janstrauss1 (5)
  • ramiromagno (3)
  • csortu (1)
  • MichelMoser (1)
  • epruesse (1)
  • alexstaj (1)
  • LucasFVoges (1)
  • prhutchi (1)
  • kosmoz (1)
  • JackieMium (1)
  • GA-Goig (1)
Pull Request Authors
  • aw1231 (1)
  • kosmoz (1)
Top Labels
Issue Labels
enhancement (2) bug (1) help wanted (1) duplicate (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 344 last-month
  • Total dependent packages: 3
  • Total dependent repositories: 4
  • Total versions: 11
  • Total maintainers: 1
cran.r-project.org: RDML

Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format Files

  • Versions: 11
  • Dependent Packages: 3
  • Dependent Repositories: 4
  • Downloads: 344 Last month
Rankings
Forks count: 8.7%
Dependent packages count: 10.9%
Stargazers count: 11.8%
Dependent repos count: 14.6%
Average: 16.4%
Downloads: 35.9%
Maintainers (1)
k.blag@yandex.ru
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • R6 >= 2.0.1 imports
  • checkmate >= 1.6.2 imports
  • data.table * imports
  • lubridate >= 1.6.0 imports
  • pipeR * imports
  • readxl * imports
  • rlist >= 0.4 imports
  • stringr * imports
  • tools >= 3.2 imports
  • xml2 >= 1.0 imports
  • MBmca * suggests
  • V8 * suggests
  • chipPCR * suggests
  • dplyr * suggests
  • ggplot2 * suggests
  • kfigr * suggests
  • knitr * suggests
  • magrittr * suggests
  • qpcR * suggests
  • reshape2 * suggests
  • shiny * suggests
  • shinyMolBio * suggests
  • shinyjs * suggests
  • shinythemes * suggests
  • testthat * suggests