index.Rmd

---
title: "Differential Expression Workshop NCGR"
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: |
  This is the material for a Differential Gene Expression workshop offered by NCGR in collaboration
  with NM-INBRE.
link-citations: yes
github-repo: ncgr/DE-Bookdown
---

# License and Copyright{-}

Creative Commons Attribution-NonCommercial-NoDerivatives 4.0
https://creativecommons.org/licenses/by-nc-nd/4.0/

© 2023 National Center for Genome Resources

<br>

![](./Figures/INBRE_Logo_Grad_transparent-2019.png){width=20%} 

<br>

![](./Figures/ncgr.png){width=30%} 

## Getting Started{-}

## Prerequisites

Unix, sequencing basics and other study guides will be provided upon acceptance.

## Installs

Make sure the following software is installed on your local computer before the workshop. Please contact Ethan Price at inbre\@ncgr.org if you have questions.


Computer requirements:\
Windows 7, 8, 10 or later \
Mac Sierra or later\
(No Chromebooks) 


1. [Zoom](https://zoom.us/download)

Install the correct version for your OS. Don't plan to use the web version, as this does not have enough features. 

2. [Integrated Genomics Viewer (IGV)](https://software.broadinstitute.org/software/igv/download)

3. [MobaXterm](https://mobaxterm.mobatek.net/download.html) (Windows Users Only. Mac or Linux users will use their native terminal)

* Download the "Home" "Installer" edition.  Be careful not to install the portable or professional editions.  

* Before installing, extract the installer zip folder to any location on your computer.  

* Now run the installer and follow the prompts.

4. [Filezilla](https://filezilla-project.org/)

5. [Cytoscape](https://cytoscape.org/)

Everyone will need Cytoscape (a web-based pathway analysis tool).  Please perform the following:

* Download Cytoscape: instructions at https://cytoscape.org/ >Download. 

* Request a ClueGo license key (this takes a couple days) at http://www.ici.upmc.fr/cluego/cluegoLicense.shtml

* Open Cytoscape 

* Install the ClueGo App. Click on Apps > App Manager > Find ClueGo in the App Manager list and click install 

* Open ClueGo in Cytoscape by clicking on Apps>ClueGo. Input your license key.


## Agenda


[Zoom](https://us06web.zoom.us/j/6272683319?omn=86109658022)

ID: 627 268 3319

Passcode: 054689

Sessions are from 9-12 and 1-4 mountain time (M-F). Please let us know (inbre@ncgr.org or during the workshop) if you have to miss part of a day.

Zoom recordings:
Please do not share these (see the Wrap Up chapter for more information).

_____


**Monday**

<span style="color: lightgray;">MORNING</span>\

NCGR and NM-INBRE Introduction (Joann)\

Student Introductions\
 

Linux\
<span style="color: forestgreen;">Linux</span> (Adam)


<span style="color: lightgray;">AFTERNOON</span>\


<span style="color: forestgreen;">Linux</span> (cont) (Adam)


_____

**Tuesday**

<span style="color: lightgray;">MORNING</span>\

<span style="color: forestgreen;">Linux</span> (cont) (Adam)

<span style="color: forestgreen;">Sequence Metrics and Quality Control</span> (Adam)\



<span style="color: lightgray;">AFTERNOON</span>\

Sequencing Technologies and Lab Protocols (Adam)

<span style="color: forestgreen;">Read Alignment</span> (indexing) (Adam)\

_____

**Wednesday**

<span style="color: lightgray;">MORNING</span>\

<span style="color: forestgreen;">Read Alignment</span> (Adam)\

<span style="color: forestgreen;">Abundance Estimation</span> (Joann)\ 


<span style="color: lightgray;">AFTERNOON</span>\

Differential Gene Expression Analysis (Joann)\
<span style="color: forestgreen;">DGE</span>


_____

**Thursday**

<span style="color: lightgray;">MORNING</span>\

Differential Gene Expression Analysis (Joann) \
<span style="color: forestgreen;">DGE (cont)</span>

<span style="color: forestgreen;">ggplot2</span> (Adam)\


<span style="color: lightgray;">AFTERNOON</span>\

<span style="color: forestgreen;">ggplot2 (cont) </span> (Adam)\

<span style="color: forestgreen;">Interactive Visualization</span> (Adam)\

_____

**Friday**

<span style="color: lightgray;">MORNING</span>\

<span style="color: forestgreen;">Pathway Enrichment Analysis</span> (Joann)\


<span style="color: lightgray;">AFTERNOON</span>\

<span style="color: forestgreen;">Coexpression Networks</span> (Joann)\

Feedback Survey\

Logrus Access Request\

_____

<span style="color: forestgreen;">Green</span> text indicates hands-on sessions. Please note that the timing might shift slightly.


## Connecting to the linux server

1. Open your terminal.

2. Type the following on your command line, substituting in your username for <username>.

```
ssh -p2403 <username>@inbre.ncgr.org
```

3. Enter your password.

If you have trouble connecting, please contact Ethan Price at inbre@ncgr.org.



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