mariusrueve / scrnaseq_app

UNDER DEVELOPMENT: Shiny app for visualisation of scRNASeq data

scrnaseq_app

A shiny app to generate and download plots
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Table of Contents

• About the Project
  • Built With
• Usage
  • Upload .rds file
  • Select genes
    • Select genes through UI
    • Select genes through an excel file with header
    • Select genes through an excel file without header
• Getting Started
• Contributing
• Contact
• Acknowledgements

About The Project

Built With

• R
• Shiny from RStudio
• Seurat

Usage

To get the app running you need to follow these simple steps.

Upload .rds file

First you need to upload a .rds file containing your Seurat object. If you don't have this file, you can use this example.

Select genes

Select genes through UI

Once the .rds file is uploaded and processed, you can click on the field below Genes and select your genes by clicking or searching. To delete genes you have to click on the gene and hit the backspace key.

Select genes through an excel file with header

You can select genes by uploading an .xlsx file (example).
The spreadsheet has to look something like this:

EnemblIDs	Genes
First ID	First Gene
Second ID	Second Gene

The app will only read the first column where it expects EnsemblIDs, whereas the column Genes is optional.

Select genes through an excel file without header

If your .xlsx file contains no header please uncheck the checkbox. Otherwise the first row/ EnsemblID will not show up in the selection.

Aspect Ratio

In order to change the aspect ratio of the plots you can change the pixels of the X and Y-Axis. By clicking on Default settings for axes the default settings will be restored: X = 1024pxand Y = 576px

Download

Once the plots are generated you can download them. The download is an archive which contains a PDF and PNG version of the selected plots. If you want to rename your archive before downloading, you can do so in the given field.

Getting Started

Installation

Singularity

If you are in the network of the MHH, you can use this link

Local

This is an example of how you may give instructions on setting up your project locally. To get a local copy up and running follow these simple example steps.

1. Clone the repo

git clone https://github.com/MHH-RCUG/scrnaseq_app

Contributing

Contributions are what make the open source community such an amazing place to be learn, inspire, and create. Any contributions you make are greatly appreciated.

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

Contact

Project Link: https://github.com/MHH-RCUG/scrnaseq_app

Acknowledgements

• scrnaseq
• README-Template