index.Rmd

--- 
title: "RNAseq Workshop"
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: |
  RNAseq analysis overview and interpretation
link-citations: yes
github-repo: https://github.com/MonashBioinformaticsPlatform/RNAseq_workshop_2024
---
***

# Getting started  

    
- **[All communications and important links will be in this Drive Document](https://docs.google.com/document/d/1jykhTx23IHoTJvu6rCcs6_cuPznlMLYQZqih_C2-kfs/edit)**


- **Instructors:** Adele Barugahare, Nitika Kandhari, Scott Coutts, Andrew Perry, Paul Harrison, Laura Perlaza-Jimenez


## Schedule

This workshop is 2 sessions long, each 4 hours

**First Day**

|  Time       |  Content                  |
|:---:|:---:|
| 10:00 | Getting started and introduction |
| 10:10 | Planning an RNAseq Experiment |
| 11:00 | Experimental Design |
| 11:20 | 00:10 Break |
| 11:30 | Library Preparation |
| 12:40 | 00:20 Lunch Break |
| 13:00 | Pipeline Overview |
| 14:00 | End of first session |

**Second Day**

|  Time       |  Content                  |
|:---:|:---:|
| 10:00 | Pipeline Overview |
| 11:20 | 00:10 Break |
| 11:30 | Pipeline Overview |
| 12:00 | Differential Expression |
| 12:40 | 00:20 Lunch Break |
| 13:00 | Differential Expression |
| 14:00 | End of second session |


## Summary

This workshop is aimed at researchers who are looking to design, analyze, and interpret bulk RNA-seq experiments without the need for coding. It is particularly suitable for those who want to:

- Develop a strong understanding of RNA-seq experiment planning and data analysis.
- Use web-based tools to process and interpret RNA-seq data.
- Gain confidence in making informed decisions about experimental design and data interpretation.


**Contact**   
Please email bioinformatics.platform@monash.edu for more information



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

# So that renv includes these in the lock file
library('xml2')
library('downlit')
```