This application allows the user to investigate datasets that include Defective Interfering Particles. It provides different analyses about the delVGs of these particles.
As a first step the right R version (3.6.3) and some additional packages need to be installed. These additional libraries are listed here:
- DT 0.33
- ggplot2 3.5.0
- hash 2.2.6.3
- jsonlite 1.8.8
- plotly 4.10.4
- plyr 1.8.9
- shiny 1.8.1.1
- shinydashboard 0.7.2
- shinyvalidate 0.1.3
- stringr 1.5.1
- dplyr 1.1.4
- Biostrings 2.62.0
- ComplexHeatmap 2.10.0
The libraries can be installed by running the following command from the root folder:
sudo bash setup_script.sh
For further support on the installation of specific libraries please use the original documentation of the corresponding library.
To run the application locally type the following command into the commandline.
bash run_DIP-DSA_local.sh
It will automatically open the application on http://localhost:8161.
Alternatively a docker container can be built to deploy the application. The commands for this are given in docker_commands.sh. It builds the container and runs it locally.
bash docker_commands.sh
It will automatically open the application on http://localhost:8161.
When uploading a custom data set the user has to provide the data in a specific format. It is a csv file with four columns. Correct ordering of the columns is crucial! For more information about the content see the following table:
| Column1 | Column2 | Column3 | Column4 | |
|---|---|---|---|---|
| header names | Segment | Start | End | NGS_read_count |
| column data type | character | integer | integer | integer |
| description | Name of the segment that the DI RNA is comming from | Start position of the deletion site | End position of the deletion site | Number of counts in the NGS data of the specific DI RNA sample |