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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

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

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. 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:

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Acknowledgements:

About

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

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