MSM guest lecture on R

Github: https://github.com/hongqin/MSM-guest-lecture

1.What is R? 

Wikipedia entry on R

Why R by Courtney Brown at Emory. 

Why R and beyond.

R blogger that provides recent and often interesting development about R.  

What is R video.

2. Install R to your own computers.

Instructions to download R. 

Install R studio.  RStudio provides a nice GUI to R.

Install packages to R: Video for Windows Version.

3. Introduction to R.

• TryR@code school
  
  
  R data camp
  
  
• Stephen J. Eglen's short intro slides. 
 
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Hong Qin's slides: Overview of R;   Basic programming in R; Input & Output in R;

Lydon Walker, getting started with R, an accelerated primer

Coursera course

 4. Simple exercises in R.

Qin's simple.R excises.  Please select 'Raw' and 'save-as' in text format. Unfortunately, web browser seem to automatically add 'txt' to the file name, and Rstudio does not run 'txt' format.  To solve this problem, we can 'create' a new R script, and copy-paste from code from the text file.

(The workshop audience mostly reached this step).

Youtube tutorial converting Excel data to CSV and load into R. 
    The sunflow seed Excel file is here.  

5. Make solution exercise.

Write an R function to calculate how much NaCl needed for X ml of Y mM NaCl solution. 

6. Simple statistical analysis in R.

Simple regression exercise.

7. Advanced training materials.

Multiple regression demo

Hierarchical clustering using cities. Code, Video.

Laddy Gaga and clustering analysis. Code. Video.

Bioconductor workshop materials.

8. Useful R materials.

• Hong Qin's R and computational biology GitHub site

• Stephen J. Eglen's PLOS article. A quick guide to teaching R programming to computational biology students. 

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http://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf

http://www.rseek.org. 

http://addictedtor.free.fr/graphiques/. 


Newly launched interactive cloud-based R for teaching: http://www.datamind.org/


Google-developers R programming videos


Avril Coghlan's little book of R for bioinformatics.


Github's collection of free R books

R by examples

9.   For preparation for the workshop

Wireless connection, laptops, power-outlets are recommended. 

Install packages and data on flash-drives in case internet connection is slow. (This can be a problem when all participants are download at the same time.)

A flow-chart on easel can be used for clarity.

Common problem is to set R working directory.