https://github.com/nasqar/SeuratWizard

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.
https://github.com/nasqar/SeuratWizard

r seurat shiny shiny-apps single-cell single-cell-analysis single-cell-genomics single-cell-rna-seq webapplication

Last synced: 3 months ago
JSON representation

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

• Host: GitHub
• URL: https://github.com/nasqar/SeuratWizard
• Owner: nasqar
• License: gpl-3.0
• Created: 2018-10-24T10:49:06.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2019-09-24T06:52:11.000Z (over 6 years ago)
• Last Synced: 2025-05-09T18:53:24.341Z (9 months ago)
• Topics: r, seurat, shiny, shiny-apps, single-cell, single-cell-analysis, single-cell-genomics, single-cell-rna-seq, webapplication
• Language: R
• Homepage: http://nasqar.abudhabi.nyu.edu
• Size: 8.77 MB
• Stars: 13
• Watchers: 6
• Forks: 5
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

• awesome-expression-browser - SeuratWizard - web-based interactive application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat. Based on the Nasqar platform (http://nasqar.abudhabi.nyu.edu) (Software list)

README

          


![#1589F0](https://placehold.it/15/1589F0/000000?text=+) `This version is no longer supported. See ` SeuratV3Wizard `for the new version`

# SeuratWizard: R Shiny interface for Seurat single-cell analysis library

## Online/Demo:

You can try it online at http://nasqar.abudhabi.nyu.edu/SeuratWizard

## Run using docker (Recommended):

```

docker run -p 80:80 aymanm/seuratwizard

```

This will run on port 80

***

## Local Install:

```

devtools::install_github("nasqar/SeuratWizard")

```

## Run:

```

library(SeuratWizard)

SeuratWizard()

```

This will run on http://0.0.0.0:1234/ by default

To run on specific ip/port:

```

ip = '127.0.0.1'

portNumber = 5555

SeuratWizard(ip,portNumber)

```

This will run on http://127.0.0.1:5555/

## Screenshots:

![alt text](screenshots/screenshot-input.png "Input Data")

![alt text](screenshots/screenshot-vln.png "Vln Plots")

![alt text](screenshots/screenshot-biomarkers.png "Cluster Biomarkers")

## Acknowledgements:

1) Rahul Satija, Andrew Butler and Paul Hoffman (2017). Seurat: Tools for Single Cell Genomics. R package version 2.2.1\. [https://CRAN.R-project.org/package=Seurat](https://CRAN.R-project.org/package=Seurat)

2) [Satija Lab](http://satijalab.org/seurat/)