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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: Harry25R
- License: gpl-3.0
- Language: R
- Default Branch: devel
- Size: 296 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
TOP
Due to data scale differences between multiple omics data, a model constructed from a training data tends to have poor prediction power on a validation data. While the usual bioinformatics approach is to re-normalise both the training and the validation data, this step may not be possible due to ethics constrains. TOP avoids re-normalisation of additional data through the use of log-ratio features and thus also enable prediction for single omics samples.
The novelty of the TOP procedure lies in its ability to construct a transferable model across gene expression platforms and for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.
Version update includes a new CCA vs AUC plotting function (CCA_AUC_plot) and the ability to optimise lambda for sensitivity or specificity via the metric argument in TOP_model.
Owner
- Name: Harry Robertson
- Login: Harry25R
- Kind: user
- Repositories: 2
- Profile: https://github.com/Harry25R
GitHub Events
Total
- Issues event: 1
- Delete event: 2
- Issue comment event: 1
- Push event: 6
- Pull request event: 4
- Create event: 3
Last Year
- Issues event: 1
- Delete event: 2
- Issue comment event: 1
- Push event: 6
- Pull request event: 4
- Create event: 3
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Harry25R | h****1@u****u | 159 |
| Nicholas Robertson | n****r@g****m | 92 |
| Harry Robertson | 6****R | 11 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 15
- Total pull requests: 3
- Average time to close issues: about 2 months
- Average time to close pull requests: 14 minutes
- Total issue authors: 3
- Total pull request authors: 1
- Average comments per issue: 0.27
- Average comments per pull request: 0.33
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 3
- Average time to close issues: 10 months
- Average time to close pull requests: 14 minutes
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.0
- Average comments per pull request: 0.33
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- nick-robo (7)
- Harry25R (7)
- ellispatrick (1)
Pull Request Authors
- Harry25R (6)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 4,523 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: TOP
TOP Constructs Transferable Model Across Gene Expression Platforms
- Homepage: https://github.com/Harry25R/TOP
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/TOP/inst/doc/TOP.pdf
- License: GPL-3
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Latest release: 1.8.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- CCA * imports
- CPOP * imports
- ClassifyR * imports
- Hmisc * imports
- caret * imports
- directPA * imports
- doParallel * imports
- dplyr * imports
- ggnewscale * imports
- ggplot2 * imports
- ggraph * imports
- ggrepel * imports
- ggthemes * imports
- glmnet * imports
- latex2exp * imports
- limma * imports
- methods * imports
- pROC * imports
- plotly * imports
- purrr * imports
- reshape2 * imports
- stats * imports
- stringr * imports
- survival * imports
- tibble * imports
- tidygraph * imports
- tidyr * imports
- utils * imports