wilson
WIlsON: Webbased Interactive Omics visualizatioN. This is a mirror of
Science Score: 23.0%
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
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
10 of 10 committers (100.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.3%) to scientific vocabulary
Repository
WIlsON: Webbased Interactive Omics visualizatioN. This is a mirror of
Basic Info
- Host: GitHub
- Owner: loosolab
- License: other
- Language: R
- Default Branch: master
- Homepage: https://gitlab.gwdg.de/loosolab/software/wilson
- Size: 923 KB
Statistics
- Stars: 2
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
WIlsON: Webbased Interactive Omics visualizatioN - The R Package
Abstract
Objective
High-throughput (HT) studies of complex biological systems generate a massive amount of so called omics data. The results are typically summarized using spreadsheet like data formats. Visualization of this data is a key aspect of both, the analysis and the understanding of biological systems under investigation. While users have many visualization methods and tools to choose from, the challenge is to properly handle these tools and create clear, meaningful, and integrated visualizations based on pre-processed datasets.
Results
The WIlsON R package employs the R Shiny and Plotly web-based frameworks using a client-server based approach comprising a range of interface and plotting modules. These can be joined to allow a user to select a meaningful combination of parameters for the creation of various plot types (e.g. bar, box, line, scatter, heat). The modular setup of elements assures a concise code base and simplifies maintenance. An app thus created can be mounted on an R Shiny Server or inside R Studio. Data must be supplied server-side using a custom tab-delimited format derived from the SummarizedExperiment format (Clarion) and can principally originate from any analysis (e.g. RNA-Seq, ChIP-Seq, Mass Spectrometry, Microarray) that results in numeric data (e.g. count, score, log2foldchange, zscore, pvalue) attributed to a feature (e.g. gene, transcript, probe, protein).
Conclusions
The WIlsON R package includes a toolbox of R Shiny modules that can be used to construct a wide array of web-interfaces for plotting feature-based data.
Availability
All components of the WIlsON R package have been implemented in an integrated web application that is available for download from the Github repository wilson-apps and can be tested on our official demonstration server.
Usage instructions can be found in the extensive documentation.
Get a Docker container here.
Please make sure to check our other projects at loosolab.
Organization and Philosophy
Visualizations are organized hierarchically as Shiny modules, such that larger visualizations are built from small, general, and reusable components.
Installation
The module source code is made available as an R package and can be installed locally with
r
install.packages("BiocManager")
BiocManager::install("wilson")
On Windows, make sure that Rtools are available. Only versions < 2.3.1.
To enable interactive plot downloads install Orca.
CLARION input format
CLARION: generiC fiLe formAt foR quantItative cOmparsions of high throughput screeNs
CLARION is a data format especially developed to be used with WIlsON, which relies on a tab-delimited table with a metadata header to describe the following columns. It is based on the Summarized Experiment format and supports all types of data which can be reduced to features and their annotation (e.g. genes, transcripts, proteins, probes) with assigned numerical values (e.g. count, score, log2foldchange, z-score, p-value). Most result tables derived from RNA-Seq, ChIP/ATAC-Seq, Proteomics, Microarrays, and many other analyses can thus be easily reformatted to become compatible without having to modify the code of WIlsON for each specific experiment.
Please check the following link for details considering the CLARION format.
How to cite
Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M. WIlsON: Webbased Interactive Omics VisualizatioN. (2018), doi: https://doi.org/10.1093/bioinformatics/bty711
License
This project is licensed under the MIT license.
Owner
- Name: Looso bioinformatics lab
- Login: loosolab
- Kind: organization
- Location: Bad Nauheim, Germany
- Website: http://www.mpi-hlr.de/index.php?id=47
- Repositories: 8
- Profile: https://github.com/loosolab
Group of bioinformatics at the Max Planck Institute for Heart and Lung Research
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Schultheis | h****t@k****e | 347 |
| Jens Preussner | j****r@m****e | 16 |
| hendrik.schultheis | h****s@m****e | 13 |
| renewiegandt | r****t@m****e | 11 |
| HendrikSchultheis | H****s@m****e | 8 |
| Jens Preußner | J****r@m****e | 5 |
| Carsten Kuenne | C****e@m****e | 3 |
| René Wiegandt | b****i@K****e | 2 |
| bioi | b****i@K****e | 2 |
| carsten.kuenne | c****e@m****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: 16 days
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 4.0
- Average comments per pull request: 0
- Merged pull requests: 0
- 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
- veritasnondatur (1)
Pull Request Authors
Top Labels
Issue Labels
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Packages
- Total packages: 1
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Total downloads:
- cran 279 last-month
- Total docker downloads: 21,613
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
cran.r-project.org: wilson
Web-Based Interactive Omics Visualization
- Homepage: https://github.com/loosolab/wilson/
- Documentation: http://cran.r-project.org/web/packages/wilson/wilson.pdf
- License: MIT + file LICENSE
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Latest release: 2.4.2
published over 5 years ago
Rankings
Maintainers (1)
Dependencies
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- DESeq2 * imports
- DT >= 0.3 imports
- FactoMineR * imports
- R6 * imports
- RColorBrewer * imports
- RJSONIO * imports
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- colourpicker * imports
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- factoextra * imports
- ggplot2 * imports
- ggrepel >= 0.6.12 imports
- gplots * imports
- grDevices * imports
- grid * imports
- heatmaply >= 0.14.1 imports
- log4r * imports
- methods * imports
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- plotly > 4.8.0 imports
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- rje * imports
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- shinyjs *
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- zip *