PCRedux
PCRedux: A Quantitative PCR Machine Learning Toolkit - Published in JOSS (2022)
Science Score: 95.0%
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○CITATION.cff file
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✓codemeta.json file
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✓DOI references
Found 3 DOI reference(s) in README and JOSS metadata -
○Academic publication links
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1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Repository
quantitative PCR machine learning helper tool
Basic Info
- Host: GitHub
- Owner: PCRuniversum
- License: other
- Language: TeX
- Default Branch: master
- Size: 93.4 MB
Statistics
- Stars: 8
- Watchers: 4
- Forks: 9
- Open Issues: 2
- Releases: 1
Metadata Files
README.md
PCRedux
Quantitative PCR Machine Learning Toolkit
The software extracts features from amplification curve data of quantitative Polymerase Chain Reactions (qPCR) (Pabinger S. et al., 2014) for machine learning purposes. Helper functions prepare the amplification curve data for processing as functional data (e.g., Hausdorff distance) or enable the plotting of amplification curve classes (negative, ambiguous, positive). The hookreg() and hookregNL() functions (Burdukiewicz M. et al., 2018) can be used to predict amplification curves with an hook effect-like curvature. The pcrfit_single() function can be used to extract features from an amplification curve.
Installation
PCRedux is available on CRAN. However, you can install the latest development version of the code using the following code:
R
library("devtools")
install_github("PCRuniversum/PCRedux")
Manual
The manual is available online.
Owner
- Name: PCRuniversum
- Login: PCRuniversum
- Kind: organization
- Repositories: 9
- Profile: https://github.com/PCRuniversum
JOSS Publication
PCRedux: A Quantitative PCR Machine Learning Toolkit
Authors
Autonomous University of Barcelona, Bellaterra, Spain, Medical University of Białystok, Białystok, Poland
Soilytix GmbH, Hamburg, Germany
Warsaw University of Technology, Warsaw, Poland
Pirogov Russian National Research Medical University, Moscow, Russia
BTU Cottbus–Senftenberg, Faculty of Health Brandenburg, Senftenberg, Germany, BTU Cottbus–Senftenberg, Faculty Environment and Natural Sciences, Senftenberg, Germany
Editor
Charlotte Soneson
Tags
qPCR bioinformatics machine learning reproducible researchGitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| devSJR | s****r@b****e | 374 |
| michbur | m****z@g****m | 122 |
| Konstantin Blagodatskikh | k****g@y****u | 14 |
| devSJR | s****r@d****g | 5 |
| Dominik Rafacz | d****z@s****l | 3 |
| Charlotte Soneson | c****n@g****m | 2 |
| Andrej-Nikolai Spiess, PhD | d****s@g****m | 2 |
| DTGT | t****8@g****m | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 7
- Total pull requests: 8
- Average time to close issues: 5 days
- Average time to close pull requests: 3 days
- Total issue authors: 6
- Total pull request authors: 3
- Average comments per issue: 3.57
- Average comments per pull request: 0.13
- Merged pull requests: 7
- 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
Top Authors
Issue Authors
- markziemann (2)
- lcolumbo (1)
- ramiromagno (1)
- jaybee84 (1)
- vondoRishi (1)
- kablag (1)
Pull Request Authors
- michbur (4)
- PrzeChoj (2)
- csoneson (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 3.5.0 depends
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