https://github.com/jasdumas/shinygeo
Gene Expression Omnibus Analysis with Shiny :microscope:
https://github.com/jasdumas/shinygeo
bioinformatics data-visualization gene-expression r shiny
Last synced: 7 months ago
JSON representation
Gene Expression Omnibus Analysis with Shiny :microscope:
- Host: GitHub
- URL: https://github.com/jasdumas/shinygeo
- Owner: jasdumas
- License: other
- Created: 2015-05-01T00:52:11.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2022-06-02T00:37:44.000Z (over 3 years ago)
- Last Synced: 2024-11-13T15:49:16.079Z (11 months ago)
- Topics: bioinformatics, data-visualization, gene-expression, r, shiny
- Language: CSS
- Homepage: http://jasdumas.com/shinyGEO/
- Size: 359 MB
- Stars: 41
- Watchers: 7
- Forks: 47
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://travis-ci.org/jasdumas/shinyGEO)
[](https://codecov.io/github/jasdumas/shinyGEO?branch=master)
# shinyGEO
shinyGEO is a web-based tool that allows a user to download the expression and sample data from a [Gene Expression Omnibus](http://www.ncbi.nlm.nih.gov/geo/browse/) dataset, select a gene of interest, and perform a survival or differential expression analysis using the available data. For both analyses, shinyGEO produces publication-ready graphics and generates R code ensuring that all analyses are reproducible. The tool is developed using shiny, a web application framework for R, a language for statistical computing and graphics.
## Official Website
http://gdancik.github.io/shinyGEO/
## How to install this package?
Install the development version from Github:
```r
library(devtools)
install_github("jasdumas/shinyGEO")
library(shinyGEO)
```
## How to use this package?
Update the series and platform meta-data:
```r
shinyGEO::updateGEOdata()
```
Launch the shiny application locally:
```r
shinyGEO::runshinyGEO()
```
Or launch the shiny application in a web browser:
[http://bioinformatics.easternct.edu/shinyGEO/](http://bioinformatics.easternct.edu/shinyGEO/)
## Contributors
- Main contributors: Jasmine Daly, Michael Gargano, Garrett M. Dancik, PhD
- Additional contributors: Ken-Heng Liao, Gregory Harper, Brandon Spratt
Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
## Acknowledgements
This work was supported, in part, by [Google Summer of Code funding to JD in 2015](https://www.google-melange.com/archive/gsoc/2015/orgs/rproject/projects/jasdumas.html). MG, KHL, GH, and BS contributed as part of an independent study in Computer Science / Bioinformatics while undergraduate students at Eastern Connecticut State University, Willimantic, CT, USA.
## Learn more
- Read the abstract about `shinyGEO` published in [*Bioinformatics*](https://academic.oup.com/bioinformatics/article-abstract/32/23/3679/2525634/shinyGEO-a-web-based-application-for-analyzing).
## Meta
- Please [report any issues or bugs](https://github.com/jasdumas/shinyGEO/issues).
- License: MIT
- Get citation information for `shinyGEO` in R doing `r citation(package = 'shinyGEO')`