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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.

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Adding Code Blocks

Run R

#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:

print(x+y)
## [1] 3
print(z)
## [1] 3.142857
n = z^y

print(n)
## [1] 9.877551

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.


ssh -h

Text and bullet lists

Put text here. Separate paragraphs by multiple lines

Bullet List:

  • first
  • second
  • third
  • fourth