Seminar III: R/Bioconductor

LCG

This course will be taught at the Undergraduate Program on Genomic Sciences (LCG in Spanish) from the National Autonomous University of Mexico (UNAM in Spanish). It is directed at the third semester students from the sixth generation. It is meant as a Bioconductor overview course and its official name is Seminar III. It has an official length of 32 class hours. For more information on this undergraduate program visit LCG's main page. For example, the sections on Development of the Genomic Sciences in Mexico and LCG's International Evaluation could be of your interest.

Home

This is the official course page for Seminar III: R/Bioconductor. Here you can find the lectures, exercises, answers, data and supporting material related to the course. Please check the syllabus for a description on the course, the objectives, project outline, a sample class and the tentative class calendar.

Comments by Sandrine Dudoit

"I have already mentioned this to Rafael, but I cannot stress enough how impressed I am by the quality of the LCG program and its outstanding students.
It is truly a pleasure to work with students that have such rare dedication, sense of initiative, and enthusiasm. In particular, I am delighted to see how proficient you have become with R and Bioconductor."
The comments were mady public with her consent. Rafael Palacios is the current LCG headmaster.

OCW

This course will serve as LCG's pilot OpenCourseWare (OCW) course. Our goal is to create a course of the highest quality worthy of being an OCW course. As such, we'll video record all the classes and we will prepare all the material both in Spanish and English.

The course has begun!!! :)

lectures

In this section you can find a small description for every lecture. Additionally, you can download the lectures in PDF format, the R code and/or the .Rnw file to make the lecture files.

Class 01: review  [code]  [.Rnw] 
The first class of the semester! We'll review R, how to make plots and learn how to use the apply functions.

Class 02: bioconductor and documentation  [code]  [.Rnw] 
On this class, we'll introduce you to Bioconductor, learn to make a basic heatmap and foment reproducible research through vignette files using Sweave.

Class 03: advanced plotting  [code]  [.Rnw] 
We'll learn how to make advanced plots using the lattice, plotrix, ggplots2 and car packages.

Class 04: public data  [code]  [.Rnw] 
We'll learn how to download public data using biomaRt, GEOquery, ArrayExpress, annotate and KEGGSOAP.

Class 04: public data  [code]  [.Rnw] 
RMySQL, AnnotationDbi, RSQLite. Short one because I got sick >.<

Class 06: genomic plots  [code]  [.Rnw] 
GenomeGraphs.

Class 07: microarrays  [code]  [.Rnw] 
Limma.

Class 08: biostrings  [code]  [.Rnw] 
Biostrings by José Reyes.

Class 09: ShortRead  [code]  [.Rnw] 
ShortRead by Alejandro Reyes.

Class 10: packages  [code]  [.Rnw] 
Packages.

Class 11: GOs  [code]  [.Rnw] 
GO.

Class 12: affy  [code]  [.Rnw] 
Stats and affy by Víctor Moreno.

Class 13: microarrays II  [code]  [.Rnw] 
Advanced Microarrays class by Víctor Moreno.

Class 14: a simulated HTS case study  [code]  [.Rnw] 
Formatdb, blastall, Velvet, Bowtie... all in a simulated case study :)

quizzes and exercises

Here you can find the quizzes and exercises to test your knowledge and skills in statistics, R and Bioconductur ^^.

Exercise 01 [code] 
Exercises for the first class (review session). They include some basic review exercises, plots and using the apply family.

Exercise 02 [code] 
Exercises for the second class. First steps into using Sweave and exploring the ALL dataset. They are also on the related lecture.

Exercise 03 [code] 
Exercises for the third class.

Exercise 04 [code] 
Exercises for the fourth class.

Exercise 06 [code] 
Exercises for the sixth class.

Exercise 08  
Exercises for the eight class.

Exercise 09  
Exercises for the ninth class.

answers

Here you can find the expected answers to the exercises. If you don't understand something, please let us know thorugh the forum. Thank you!

01_answer_review.pdf [code] 
File with the expected answers for the 1st set of exercises.

02_answer_sweave.pdf [code] 
File with the expected answers for the 2nd set of exercises.

03_answer_advplots.pdf [code] 
File with the expected answers for the 3rd set of exercises.

answer_04_biomart.pdf [code] 
File with the expected answers for the 4th set of exercises version b.

answer_05_rmysql.pdf [code] 
File with the expected answers for the 5th set of exercises.

answer_06_genome.pdf [code] 
File with the expected answers for the 6th set of exercises.

respuesta.pdf 
File with the expected answers for the 8th set of exercises.

data

Here you can find the data sets that we'll use in the classes and exercises.

stats.txt
A Velvet output file that contains information on contigs from simulated E. coli reads.

SuppTable01_kogenome6_double_end-clone_1132_742.csv
A supplementary table from http://www.ncbi.nlm.nih.gov/pubmed/19587683 in csv format.

SuppTable06_nsSnp_AK1.csv
A supplementary table from http://www.ncbi.nlm.nih.gov/pubmed/19587683 in csv format.

swirl
Swirl data.

areyes
Data for the ShortRead exercise.

jmoreno
Data for the affy exercise by Víctor Moreno.

jmoreno2
Data for the second affy exercise by Víctor Moreno.

simulated HTS case study
Data for the last class.

videos

In this section you can find the class videos. We'll upload them with a week delay due to the video processing procedure.

lcollado20090814.flv
Video record of the first class :) It's 1hr 14 mins 59 seconds long and is available on flv format as a 113 MB file.

lcollado20090821.mpg
Video record of the second class. It's available on mpg format as a 390 MB file.

lcollado20090821.flv
Video record of the second class. It's available on flv format as a 143 MB file.

lcollado20090828.flv
Video record of the third class. It's available on flv format as a 353 MB file.

lcollado20090904.flv
Video record of the fourth class. It's available on flv format as a 359 MB file.

lcollado20090917.flv
Video record of the sixth class. It's available on flv format as a 259 MB file.

lcollado20090925.flv
Video record of the seventh class. It's available on flv format as a 339 MB file.

download

We recommend you to download the videos by right clicking the link and choosing "save link as". Then use your prefered video player to watch the videos.

thanks

We thank the support of the UATI group at LCG to record, edit and create the final video files.

package overviews

In this section you can find the brief package overview presentations made by the students.

Expo.pdf  [code]  
Jorge Buendia's geneplotter overview.

PACKAGE.pdf  [code]  txt with results 
Lisandra Zepeda's qvalue overview.

Biostrings.pdf  [code]  
Isaac Lopez's Biostrings overview.

Package.pdf  [code]  
Mariana Ruiz's Hardy-Weinberg overview.

GeneR-avargas.pdf  [.Rnw]  
Amhed Vargas's GeneR overview.

GeneR_1.pdf  
Jorge Zepeda and Fabricio López's GeneR overview.

expo_-1-_1.pdf  
Marco Ortiz and Augusto Berrocal's RmirR overview.

HTqPCR_2.pdf  [.R]  [pdf vignette style]  
Daniela García and Yuvia Pérez's HTqPCR overview.

patter_1.pdf  [.R]  [.Rnw]  
Ricardo Moreno and Melvin Noé's Splicegear overview.

expoMAIN_RUN_1.pdf  [.R]  
Yael Fonseca and Héctor Medina's COSMO overview.

gladglad_1.pdf  
Francisco Diaz and José Samaniego's GLAD overview.

mayepresent_1.pdf  
Luz Mayela's Rolexa overview.

credits

These were made thanks to the students :) and all credit goes to them.

supporting material

Here you can find links to different pdf files or urls which we used to create this course or that can help you as a reference.

R language definition 

An Introduction to R 

An Easy Introduction to R 

The Not so Short Introduction to LaTeX 

Beamer Userguide 

Symbols in LaTeX 

websites

Here you can find several websites useful for and as reference for Statistics, R and/or Bioconductor.

Bioconductor's main site 

Bioconductor's official workshops 

Programming in R -- tgirke 

Producing Simple Graphs with R 

Peter's R Programming Pages  

Programming in R -- zoonek  

Quick-R for SAS/SPSS/Stata Users 

books

Here you can find several books on Statistics, R and/or Bioconductor.

Günther Sawitzki (2009).
Computational Statistics: An Introduction to R.
CRC Press

Robert Gentleman (2008).
R Programming for Bioinformatics.
CRC Press

John Chambers (2008).
Software for Data Analysis: Programming with R.
Springer

R. Gentleman, V. Carey, W. Huber, R. Irizarry, and S. Dudoit (2005).
Bioinformatics and Computational Biology Solutions Using R and Bioconductor.
Springer

F. Hahne, W. Huber, R. Gentleman, and S. Falcon (2008).
Bioconductor Case Studies.
Springer

John Verzani (2005).
UsingR for Introductory Statistics.
Chapman & Hall-CRC.

John Maindonald and John Braun (2007).
Data Analysis and Graphics Using R - an Example-Based Approach.
Cambridge University Press.

Deborah Rumsey (2003).
Statistics for Dummies.
Wiley Publishing, Inc.

Bernard Rosner (2006).
Fundamentals of Biostatistics.
Thomson Books/Cole.