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https://github.com/nasqar/seuratv3wizard
A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
https://github.com/nasqar/seuratv3wizard
bioinformatics r seurat shiny shiny-apps single-cell single-cell-analysis single-cell-genomics single-cell-rna-seq visualization webapp
Last synced: 19 days ago
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A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
- Host: GitHub
- URL: https://github.com/nasqar/seuratv3wizard
- Owner: nasqar
- License: gpl-3.0
- Created: 2019-02-05T06:41:47.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-09-14T11:33:15.000Z (almost 4 years ago)
- Last Synced: 2024-02-24T18:41:13.242Z (4 months ago)
- Topics: bioinformatics, r, seurat, shiny, shiny-apps, single-cell, single-cell-analysis, single-cell-genomics, single-cell-rna-seq, visualization, webapp
- Language: R
- Homepage: http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard
- Size: 10.9 MB
- Stars: 31
- Watchers: 8
- Forks: 14
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Lists
- awesome_single_cell - SeuratV3Wizard - a web-based (wizard style) interactive R Shiny application to perform guided single-cell RNA-seq data analysis and clustering based on Seurat v3. [demo](http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard/) (Web portals and apps / Interactive visualization and analysis)
- awesome-expression-browser - SeuratV3Wizard - successor of `SeuratWizard` (above) for Seurat v3 (Software list)
- awesome-single-cell - SeuratV3Wizard - a web-based (wizard style) interactive R Shiny application to perform guided single-cell RNA-seq data analysis and clustering based on Seurat v3. [demo](http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard/) (Web portals, apps, and databases / Interactive visualization and analysis)
- awesome-single-cell - SeuratV3Wizard - a web-based (wizard style) interactive R Shiny application to perform guided single-cell RNA-seq data analysis and clustering based on Seurat v3. [demo](http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard/) (Web portals, apps, and databases / Interactive visualization and analysis)
README
# SeuratV3Wizard: R Shiny interface for Seurat single-cell analysis library
## New Features:
Sep 5, 2019
- all plots can be downloaded
- file with multiple samples can be uploaded
- tsne and umap are both always calculated
Apr 25, 2019
- [Seurat v3](https://github.com/satijalab/seurat)
- [sctransform Option](https://github.com/ChristophH/sctransform)
- [UCSC Cellbrowser](https://github.com/maximilianh/cellBrowser)
## Online/Live instance:
You can try it online at http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard
## Pre-print:
[NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization](https://doi.org/10.1101/709980)
## Run using docker (Recommended):
Make sure Docker (version >= 17.03.0-ce) is installed.
```
docker run -p 80:80 aymanm/seuratv3wizard
```
This will run on port 80
To run on a different port:
```
docker run -p 8083:80 aymanm/seuratv3wizard
```
This will run on port 8083
## Local Install:
Make sure to have devtools installed first
```
devtools::install_github("nasqar/seuratv3wizard")
```
Optional: For ucsc cellbrowser support, make sure to follow the installation instructions [here](https://cellbrowser.readthedocs.io). For linux-based OS, type the following in the terminal:
```
sudo pip install cellbrowser=0.5.6
```
## Run:
```
library(SeuratV3Wizard)
SeuratV3Wizard()
```
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
SeuratV3Wizard(ip,portNumber)
```
This will run on http://127.0.0.1:5555/
## Screenshots:
## Acknowledgements:
- 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)
- [Satija Lab](http://satijalab.org/seurat/)
- [Christoph Hafemeister, Rahul Satija (2019). Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression](https://github.com/ChristophH/sctransform)
- [UCSC Single Cell Browser](https://github.com/maximilianh/cellBrowser)