---
title: "Put your page title here"
author: "Your Name"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: 
  html_document:
    theme: united
    highlight: tango
    df_print: paged
    toc: true
    toc_float: true
    toc_depth: 4
  
---


```{r setup, include=FALSE}
library(reticulate)
use_python('/path/to/python') #EDIT
knitr::opts_chunk$set(echo = TRUE)
```



[home](https://rsh249.github.io/applied_bioinformatics)


# Introduction

Applied Bioinformatics will challenge you all by teaching computational skills that are becoming essential training for biologists. This includes coding in R and Python and working with command line programs.

We will work on developing these skills in the framework of a DNA sequencing project using the Oxford Nanopore MinION sequencer. The MinION is a cutting edge device that brings DNA sequencing directly to the scientist in real-time. 

Together we will design sequencing experiments, collect data using the MinION, and build projects to analyze those data.


# Embed youtube videos:

Note that you must get the 'embed' link by clicking on the share link, or paste the video ID number after "embed/" in the URL below.

<div align="left">
<iframe width="640" height="360" src="https://www.youtube.com/embed/-IFo5Uv-9BY?rel=0"; frameborder="0" allowfullscreen></iframe>
</div>



## secondary section heading

put stuff here 

### tertiary section heading

put stuff here 

### tertiary section heading 2

put stuff here 


# Adding Code Blocks

## Run R

```{R, eval=TRUE}
#Put sections of R code here

x = 1
y = 2
z = 22/7

```

Then write explanations, commentary, or questions you have in between.

Followed by more R code:

```{R, eval = TRUE}
print(x+y)

print(z)

n = z^y

print(n)
```
## Don't run (some R, usually bash, some python)

Sometimes you don't want code to run. Maybe it does not work or it takes a long time to run. Or the scope (path, program) is not accessible.

Use 'eval=FALSE' for those code blocks.


```{bash, eval=FALSE}

ssh -h

```

## Text and bullet lists

Put text here. Separate paragraphs by multiple lines

Bullet List: 

+ first
+ second
+ third
+ fourth

# Add a Link:

Add links using brackets [] around the URL and the name to show in parentheses () [https://google.com](Google).






[home](https://rsh249.github.io/applied_bioinformatics)