https://github.com/JoachimGoedhart/VolcaNoseR
Shiny app for making and annotating Volcano plots
https://github.com/JoachimGoedhart/VolcaNoseR
dataviz genomic-data-analysis ggplot2 proteomics-data-analysis shiny shinyapp volcano
Last synced: 4 months ago
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Shiny app for making and annotating Volcano plots
- Host: GitHub
- URL: https://github.com/JoachimGoedhart/VolcaNoseR
- Owner: JoachimGoedhart
- License: gpl-3.0
- Created: 2020-01-13T20:52:04.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2022-11-21T19:30:46.000Z (over 2 years ago)
- Last Synced: 2024-08-13T07:14:28.992Z (8 months ago)
- Topics: dataviz, genomic-data-analysis, ggplot2, proteomics-data-analysis, shiny, shinyapp, volcano
- Language: R
- Homepage: https://huygens.science.uva.nl/VolcaNoseR/
- Size: 472 KB
- Stars: 20
- Watchers: 3
- Forks: 7
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- jimsghstars - JoachimGoedhart/VolcaNoseR - Shiny app for making and annotating Volcano plots (R)
README
# VolcaNoseR
A Shiny App for making Volcano plots
### Running the App
The web-tool runs from a shiny server, and can be accessed at:
o [https://huygens.science.uva.nl/VolcaNoseR/](https://huygens.science.uva.nl/VolcaNoseR/)
o [https://huygens.science.uva.nl/VolcaNoseR2/](https://huygens.science.uva.nl/VolcaNoseR2/)
o [https://amsterdamstudygroup.shinyapps.io/VolcaNoseR/](https://amsterdamstudygroup.shinyapps.io/VolcaNoseR/)
o [https://goedhart.shinyapps.io/VolcaNoseR/](https://goedhart.shinyapps.io/VolcaNoseR/), while bandwidth lasts
Alternatively, the app can run from R/Rstudio and this is perhaps the best option for loading large files. See instructions below
#### Preparations
Note that the app depends on several R packages that need to be installed (shiny, ggplot2, dplyr, magrittr, ggrepel, DT, shinycssloaders, RCurl, readxl).
Run this command in R/Rstudio to download and install all the packages (only needs to be done once):
```
install.packages("shiny", "tidyverse", "ggrepel", "DT", "shinycssloaders", "RCurl", "readxl", "ggiraph", "htmlwidgets")
```
o The first option is running it directly from Github. In the command line (in R or Rstudio) type:
```
shiny::runGitHub('VolcaNoseR', 'JoachimGoedhart')
```
o The second option is download the app and to use it offline:
-download the `app.R` and csv files (`Data-Vulcano-plot.csv` and `elife-45916-Cdc42QL_data.csv`) with example data.
-Run RStudio and load `app.R`
-Select 'Run All' (shortcut is command-option-R on a Mac) or click on "Run App" (upper right button on the window)
This should launch a web browser with the Shiny app.
### Credits
There are several Shiny apps for Volcano plots that have served as a source of inspiration:
-[VolcanoR](https://github.com/vovalive/volcanoR)
-[Volcanoshiny](https://github.com/hardingnj/volcanoshiny)
-[VolcanoPlot_shiny_app](https://github.com/stemicha/VolcanoPlot_shiny_app)
VolcaNoseR is created and maintained by Joachim Goedhart ([@joachimgoedhart](https://twitter.com/joachimgoedhart))
### Example output
Standard output generated with the example data:
Output with user selected annotation of data:
