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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.

Ubuntu notes and codes

pwd -> print working directory

ls -> shows folders and files in working directory

ls -a -> shows files and ones hidden

ls-l -> gives date of files being last edited

man (+command) -> says what the command does

q -> quit out of window

cd -> change directory, put new place after cd

ssh -> secure shell

mkdir (name) -> make directory

touch (name) -> makes empty text file

R notes and codes

``` used to start and end data block

Knitr runs command only in data blocks, makes documents look nice

Run runs everything in the document

Adding Code Blocks

Run R

census = read.csv('/usr/share/data/kaggle/census.csv')
head(census)
library(ggplot2)
demo = census #Just rename the object for the next lines
ggplot(data = demo) +
  geom_point(mapping = aes(x = Citizen, y = TotalPop))

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