ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
5 of 17 committers (29.4%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.1%) to scientific vocabulary
Keywords from Contributors
Repository
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
Statistics
- Stars: 5
- Watchers: 2
- Forks: 4
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
ClassifyR: Performance evaluation for multi-view data sets and seamless integration with MultiAssayExperiment and Bioconductor
ClassifyR's performance evaluation focuses on model stability and interpretability. Based on repeated cross-validation, it is possible to evaluate feature selection stability and also per-sample prediction accuracy. Also, multiple omics data assays on the same samples are becoming more popular and ClassifyR supports a range of multi-view methods to evaluate which data view is the most predictive and combine data views to evaluate if multiple views provide superior predictive performance to a single data view.
Installation
The recommended method of installing ClassifyR is by using Bioconductor's BiocManager installer:
library(BiocManager)
install("ClassifyR", dependencies = TRUE)
The above code will install all packages that provide feature selection or model-building functionality. If only one or two methods are desired then the dependencies option could be omitted and those packages providing functionality installed manually.
Website
Please visit the ClassifyR website to view the main vignette as well as articles that provide more in-depth explanations for various aspects of the package. Details of performance evaluation, multi-view methods and contributing a wrapper for a new algorithm to the package are provided.
Reference
Strbenac D., Mann, G.J., Ormerod, J.T., and Yang, J. Y. H. (2015) ClassifyR: An R package for performance assessment of classification with applications to transcriptomics, Bioinformatics.
Owner
- Name: Sydney Precision Data Science Centre
- Login: SydneyBioX
- Kind: organization
- Location: Sydney, Australia
- Website: https://www.sydney.edu.au/science/our-research/research-centres/sydney-precision-data-science-centre.html
- Twitter: sydneybioinfo
- Repositories: 76
- Profile: https://github.com/SydneyBioX
SPDSC alliance brings together multiple research groups and junior and senior researchers with shared interests in bioinformatics and computational sciences.
GitHub Events
Total
- Issues event: 22
- Watch event: 1
- Issue comment event: 10
- Push event: 50
- Pull request event: 2
- Fork event: 1
- Create event: 2
Last Year
- Issues event: 22
- Watch event: 1
- Issue comment event: 10
- Push event: 50
- Pull request event: 2
- Fork event: 1
- Create event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Dario Strbenac | d****o@m****u | 197 |
| Dario Strbenac | D****c@g****u | 94 |
| Dario Strbenac | d****0@u****u | 67 |
| Ellis Patrick | e****7@g****m | 53 |
| Ellis Patrick | e****k@s****u | 37 |
| Nick | n****r@g****m | 20 |
| Nitesh Turaga | n****a@g****m | 14 |
| Dan Tenenbaum | d****a@f****g | 10 |
| Alexander Berrell | u****r@1****u | 8 |
| Herve Pages | h****s@f****g | 4 |
| peterkoch5785 | p****h@m****u | 3 |
| Hervé Pagès | h****s@f****g | 2 |
| J Wokaty | j****y@s****u | 2 |
| vobencha | v****a@g****m | 2 |
| J Wokaty | j****y | 2 |
| vobencha | v****n@r****g | 2 |
| Marc Carlson | m****n@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 8
- Total pull requests: 1
- Average time to close issues: 8 days
- Average time to close pull requests: about 3 hours
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 1
- Average time to close issues: 8 days
- Average time to close pull requests: about 3 hours
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- DarioS (8)
- Harry25R (2)
- Tenyo3435 (1)
- ellispatrick (1)
Pull Request Authors
- ellispatrick (1)
- Harry25R (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 31,128 total
- Total dependent packages: 4
- Total dependent repositories: 0
- Total versions: 20
- Total maintainers: 1
bioconductor.org: ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing
- Homepage: https://sydneybiox.github.io/ClassifyR/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/ClassifyR/inst/doc/ClassifyR.pdf
- License: GPL-3
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Latest release: 3.12.4
published 11 months ago
Rankings
Maintainers (1)
Dependencies
- BiocParallel * depends
- MultiAssayExperiment >= 1.6.0 depends
- R >= 4.1.0 depends
- S4Vectors >= 0.18.0 depends
- generics * depends
- methods * depends
- survival * depends
- dplyr * imports
- genefilter * imports
- grid * imports
- randomForest * imports
- rlang * imports
- tidyr * imports
- utils * imports
- BiocStyle * suggests
- IRanges * suggests
- PoiClaClu * suggests
- Rmixmod * suggests
- car * suggests
- class * suggests
- cowplot * suggests
- e1071 * suggests
- edgeR * suggests
- ggplot2 >= 3.0.0 suggests
- glmnet * suggests
- gridExtra >= 2.0.0 suggests
- gtable * suggests
- htmltools * suggests
- knitr * suggests
- limma * suggests
- pamr * suggests
- parathyroidSE * suggests
- randomForestSRC * suggests
- rmarkdown * suggests
- robustbase * suggests
- scales * suggests