---
title: Index of scGate vignettes
author: "M. Andreatta, Ariel J. Berenstein, S. Carmona"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Index of scGate vignettes}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

Currently available scGate vignettes:

1. A demo of the **basic functionalities** of scGate on scRNA-seq data - [scGate basics](https://carmonalab.github.io/scGate.demo/scGate.basic.usage.html) 

2. Purifying cells on multi-modal **scATAC-seq + scRNA-seq data** - [scGate ATAC+RNA](https://carmonalab.github.io/scGate.demo/scGate.ATAC-seq.html) 

3. Purifying cells on **CITE-seq data** - [scGate CITE-seq](https://carmonalab.github.io/scGate.demo/scGate.CITE-seq.html) 

4. scGate to annotate scRNA-seq datasets integrated with **Harmony** and **STACAS** - [scGate integrated](https://carmonalab.github.io/scGate.demo/scGate.integrated.html)

More information available at the [scGate repository](https://github.com/carmonalab/scGate) at on the related [publication](https://academic.oup.com/bioinformatics/article/38/9/2642/6544581).
