bioCancer
:cancer: :free: A Shiny App for Interactive Multi-OMICS Cancer Data Visualization and analysis
Science Score: 10.0%
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
2 of 8 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.9%) to scientific vocabulary
Keywords
Repository
:cancer: :free: A Shiny App for Interactive Multi-OMICS Cancer Data Visualization and analysis
Basic Info
- Host: GitHub
- Owner: kmezhoud
- License: other
- Language: R
- Default Branch: master
- Homepage: https://bioconductor.org/packages/3.14/bioc/vignettes/bioCancer/inst/doc/bioCancer.html
- Size: 829 MB
Statistics
- Stars: 21
- Watchers: 1
- Forks: 5
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
bioCancer - Interactive Multi-OMICS Cancers Data Visualization and Analysis
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bioCancer is a browser-based interface for Cancer Genomics Data analysis and visualization developped by R, and based on the Shiny package. Example of bioCancer server is hosted at http://46.101.227.???:3838/bioCancer/
Interactivities
bioCancer is listening user setting. Results are updated immediately when inputs are changed (i.e., no separate dialog boxes).
Context
bioCancer focuses on Cancer Genomics data visualisation and Genes Classifications.
Circomics: Pull User genetic profiles with existing Cancer studies
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It is inspired from radiant developed by Dr. Vincent Nijs.
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Preprocessing and Plotting
Genes Classification and Biological terms Clustering
Network modeling example
How to install bioCancer
- Required: R version 3.2 or later
- Required: A modern browser (e.g., Chrome or Safari). Internet Explorer (version 11 or higher) should work as well
- Recommended: Rstudio
bioCancer courant release:
r
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("bioCancer")
bioCancer is under development:
r
devtools::install_github("kmezhoud/bioCancer")
library("bioCancer")
When bioCancer starts you will see a table of available Cancer Studies. To close the application click on Quit in the Navigation bar and then click the Quit button on the left of the screen. The bioCancer process will stop and the browser window will close (or gray-out).
Documentation
Documentation and tutorials are available in the bioCancer web interface (the ? icons and the Help menu).
Acknowledgment
bioCancer is a collaborative work . Processing panel is adapted from radiant. I would like to thank Dr. Vincent Nijs for sharing his work for R community.
Owner
- Name: Kirus Magnus
- Login: kmezhoud
- Kind: user
- Location: Tunis
- Company: @cnstn
- Website: https://kmezhoud.netlify.app/
- Repositories: 7
- Profile: https://github.com/kmezhoud
Data Scientist
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| mostly-harmless | v****s@u****u | 1,146 |
| kmezhoud | k****d@g****m | 289 |
| kmezhoud | k****d | 9 |
| Karim Mezhoud | M****d@M****n | 8 |
| Vincent Nijs | m****s | 6 |
| Vincent Nijs | v****s@p****) | 1 |
| mostly-harmless | v****s@s****n | 1 |
| Vincent | v****s@r****u | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- bioconductor 17,602 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: bioCancer
Interactive Multi-Omics Cancers Data Visualization and Analysis
- Homepage: https://kmezhoud.github.io/bioCancer/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/bioCancer/inst/doc/bioCancer.pdf
- License: AGPL-3 | file LICENSE
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Latest release: 1.36.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6.0 depends
- XML >= 3.98 depends
- radiant.data >= 0.9.1 depends
- AlgDesign >= 1.1.7.3 imports
- AnnotationDbi * imports
- Biobase * imports
- DOSE * imports
- DT >= 0.3 imports
- DiagrammeR <= 1.01 imports
- GO.db * imports
- R.methodsS3 * imports
- R.oo * imports
- ReactomePA * imports
- clusterProfiler * imports
- dplyr >= 0.7.2 imports
- geNetClassifier * imports
- htmlwidgets * imports
- httr * imports
- import >= 1.1.0 imports
- methods * imports
- org.Bt.eg.db * imports
- org.Hs.eg.db * imports
- plyr * imports
- reactome.db * imports
- shiny >= 1.0.5 imports
- shinythemes * imports
- tibble * imports
- visNetwork * imports
- BiocStyle * suggests
- knitr * suggests
- prettydoc * suggests
- rmarkdown * suggests
- testthat >= 0.10.0 suggests