iCOBRA
Interactive benchmarking of ranking and assignment methods
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Repository
Interactive benchmarking of ranking and assignment methods
Statistics
- Stars: 16
- Watchers: 6
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
iCOBRA - Interactive benchmarking of ranking and assignment methods
iCOBRA is a package to calculate and visualize performance metrics for
ranking and binary assignment methods. A typical use case could be,
for example, comparing methods calling differential expression in
gene expression experiments, which could be seen as either a ranking
problem (estimating the correct effect size and ordering the genes by
significance) or a binary assignment problem (classifying the genes
into differentially expressed and non-differentially expressed).
iCOBRA can be used either directly from the console, or via the
interactive shiny application (see the function COBRAapp()). It can also
be accessed from the web server http://imlspenticton.uzh.ch:3838/iCOBRA/
We have also collected a set of benchmarking data sets, addressing different aspects of genomic data analysis. The collection is reachable via the following link: http://imlspenticton.uzh.ch/robinsonlab/benchmarkcollection/
Installation
iCOBRA can be installed from Bioconductor using BiocManager:
install.packages("BiocManager")
BiocManager::install("iCOBRA")
or, optionally,
BiocManager::install("markrobinsonuzh/iCOBRA")
Quick start guide
The iCOBRA workflow starts from an object of class COBRAData,
containing (adjusted) p-values and/or scores for a set of features as
well as the true status of the features. An example data set is provided in
the package
library(iCOBRA)
data(cobradata_example)
The function calculate_performance() calculates the different performance
metrics for a COBRAData object. By default, all performance metrics are
calculated, but a subset can be selected using the aspects argument.
cobraperf <- calculate_performance(cobradata_example, binary_truth = "status",
cont_truth = "logFC",
aspects = c("fdrtpr", "fdrtprcurve",
"corr"))
Next, the performance metrics are prepared for plotting using the
prepare_for_plot() function. This function defines colors for the
various methods and can also be used for selecting only a subset of the
methods for visualization, without having to recalculate the performance metrics.
cobraplot <- prepare_data_for_plot(cobraperf, colorscheme = "Set2",
keepmethods = c("voom", "edgeR"))
The resulting object can then be used to generate plots of the selected aspects.
plot_fdrtprcurve(cobraplot)
plot_corr(cobraplot, corrtype = "spearman")
Vignette
The vignette can be found in the vignettes/ directory. Further
information is also available in the 'Instructions' tab of the shiny app.
After installation, the vignette can be accessed from the R console by typing
browseVignettes("iCOBRA")
Benchmarking data set collection
To facilitate future benchmarking studies, we have collected a set of benchmarking
data sets on http://imlspenticton.uzh.ch/robinsonlab/benchmarkcollection/. The page provides
links to raw data as well as evaluation results suitable for import into iCOBRA.
Owner
- Name: Charlotte Soneson
- Login: csoneson
- Kind: user
- Website: http://csoneson.github.io/
- Twitter: CSoneson
- Repositories: 110
- Profile: https://github.com/csoneson
GitHub Events
Total
- Watch event: 2
- Push event: 5
- Create event: 2
Last Year
- Watch event: 2
- Push event: 5
- Create event: 2
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Charlotte Soneson | c****n@g****m | 85 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| d.tenenbaum | d****m@b****8 | 4 |
| vobencha | v****a@g****m | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 2 |
| c.soneson | c****n@b****8 | 2 |
| Herve Pages | h****s@f****g | 2 |
| mikelove | m****e@g****m | 1 |
| j.hester | j****r@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 5
- Total pull requests: 2
- Average time to close issues: about 7 hours
- Average time to close pull requests: about 8 hours
- Total issue authors: 4
- Total pull request authors: 2
- Average comments per issue: 2.8
- Average comments per pull request: 1.0
- Merged pull requests: 2
- 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
- mikelove (2)
- jgilis (1)
- rob-p (1)
- koenvandenberge (1)
Pull Request Authors
- csoneson (2)
- mikelove (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 27,319 total
- Total dependent packages: 2
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: iCOBRA
Comparison and Visualization of Ranking and Assignment Methods
- Homepage: https://github.com/csoneson/iCOBRA
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/iCOBRA/inst/doc/iCOBRA.pdf
- License: GPL (>=2)
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Latest release: 1.36.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0 depends
- DT * imports
- ROCR * imports
- UpSetR * imports
- dplyr * imports
- ggplot2 >= 2.0.0 imports
- limma * imports
- markdown * imports
- methods * imports
- reshape2 * imports
- scales * imports
- shiny >= 0.9.1.9008 imports
- shinyBS * imports
- shinydashboard * imports
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/run-BiocCheck v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite