README.md

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
• sctransform Option
• UCSC 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

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:

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

• Satija Lab

• Christoph Hafemeister, Rahul Satija (2019). Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

• UCSC Single Cell Browser