Demos and tutorials for scGate

This repo contains commented notebooks to illustrate the usage of the scGate package

Start here!

A DEMO for the basic functionalities of scGate: scGate basics

For scGate installation instructions refer to the scGate repository

More demos

We will be posting here several demos for scGate usage in different scenarios:

1. A demo of the basic functionalities of scGate on scRNA-seq data - scGate basics

2. Purifying cells on multi-modal scATAC-seq + scRNA-seq data - scGate ATAC+RNA

3. Purifying cells on CITE-seq data - scGate CITE-seq

4. scGate to annotate scRNA-seq datasets integrated with Harmony and STACAS - scGate integrated

Clone the repository

To access the raw code and run these demos on your machine, you may also clone the repository:

git clone https://github.com/carmonalab/scGate.demo.git

Then open the project scGate.demo.Rproj in Rstudio and follow the commands in one of the available notebooks.