index.Rmd

--- 
title: "scRNAseq Analysis in R with Seurat"
author: 'Teams at QCIF bioinformatics, Sydney Informatics Hub (SIH), Monash Genomics and Bioinformatics Platform (MGBP)'
date: 'Compiled: `r format(Sys.Date(), "%B %d, %Y")`'
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
# url: your book url like https://bookdown.org/yihui/bookdown
# cover-image: path to the social sharing image like images/cover.jpg
description: |
  scRNAseq analysis in R with Seurat workshop material 
link-citations: yes
github-repo: https://github.com/swbioinf/scRNAseq_Workshop
---

***

# Getting started

## Summary

This workshop will cover the basics of single cell RNAseq analysis in R using [Seurat](https://satijalab.org/seurat/). 
We will run through basic preprocessing using Seurat package (based on the the [Seurat preprocessing tutorial](https://satijalab.org/seurat/articles/pbmc3k_tutorial.html)),
as well as correction of batch effects with [Harmony](https://github.com/immunogenomics/harmony) and cell annotation using [SingleR](https://bioconductor.org/packages/release/bioc/html/SingleR.html).  


If you are using virtual machine (VM) provided by the workshop, you don't need to install any R packages, and can skip the setup section.

If you are using your own computer, follow [Installation and Setup instructions](set-up.html). 


```{r include=FALSE}
# automatically create a bib database for R packages
knitr::write_bib(c(
  .packages(), 
  'bookdown', 'knitr', 'rmarkdown','stringr'
  ), 'packages.bib')
```