index.Rmd

--- 
title: "scRNAseq Analysis in R with Seurat"
author: '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/MonashBioinformaticsPlatform/Nov2023_scRNAseq_workshop
---
***

# Getting started

Instructors:  [Paul Harrison](https://www.monash.edu/researchinfrastructure/bioinformatics/about/people) & [Laura Perlaza-Jimenez](https://www.monash.edu/researchinfrastructure/bioinformatics/about/people)

## Summary

This workshop, conducted by the Monash Genomics and Bioinformatics Platform, will cover how to extend analysis to contemporary third-party tools, [Seurat](https://satijalab.org/seurat/), [Harmony](https://github.com/immunogenomics/harmony) and [SingleR](https://bioconductor.org/packages/release/bioc/html/SingleR.html). We will be walking through the Single Cell analysis using Seurat package, correction of batch effects with Harmony and cell annotation using SingleR.  

If you are using virtual machine (VM) provided by the workshop, you don't need to install any R packages. **Skip SET UP** section.

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


### Recommended Computer Requirements:

System Requirements:


*Windows:*

* Windows 8.1 (64-bit) or later
* 4GB RAM
* SSD storage highly recommended
* Updated video/display drivers recommended


*macOS:*

* macOS 10.15 (Catalina) or later
* 4GB RAM
* SSD storage highly recommended

Install latest versions of:

* R
* RStudio
* Seurat
* SeuratWrappers
* SingleR
* Celldex
* Harmony



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