Question: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
38
gravatar for Michael Dondrup
7.5 years ago by
Bergen, Norway
Michael Dondrup43k wrote:

I have been asked to recommend introductory books and resources to R and Bioconductor. My problem is just, I never read a book to learn R or Bioconductor, so I have no experience with this and cannot recommend one. I am interested in mainly introductory books, possibly targeting various groups of readers (computer scientists, molecular biologists, (bio-)statisticians), any recommendation appreciated.

For example, I used the following resources:

Which books did you find helpful or completely useless to learn R/Bioconductor? For example: R Programming for Bioinformatics looks promising, anybody read it?

Or do you share my reluctance towards R-books and prefer online resources?

R bioconductor books • 14k views
ADD COMMENTlink modified 2.9 years ago by Parham1.3k • written 7.5 years ago by Michael Dondrup43k
28
gravatar for Jeremy Leipzig
7.5 years ago by
Philadelphia, PA
Jeremy Leipzig17k wrote:

Theresa Scott's Intro deserves a mention although it can be a bit verbose.

Introduction to the Fundamentals & Functionality of the R Programming Language

For Bioconductor and short read analysis I would stick with Girke's cookbook which I have found amazingly helpful. I would gladly have paid $100 for access to it.

Sequence Analysis with R and Bioconductor

Have not read R in a Nutshell yet but from what I saw in Joseph Adler's Baseball Hacks and the initial reviews I have a good feeling about it.

I would avoid R Programming for Bioinformatics as that book is really geared toward package development.

I co-wrote an O'Reilly Short Cut, "Data Mashups in R", that is designed to be a little more fun than some of the scientific stuff out there while still exploring data manipulation in R, using packages, XML, web services, rudimentary plotting, and even some statistics. It costs $5 if you are not a Safari subscriber.

Data Mashups in R

ADD COMMENTlink modified 15 months ago • written 7.5 years ago by Jeremy Leipzig17k
1

The Art of R Programming is a great book for both beginners and experts. It contains very few bells and whistles, but a lot of meticulous code examples and explanations.

ADD REPLYlink written 5.7 years ago by Jeremy Leipzig17k

HT Sequence Analysis with R and Bioconductor is a great resource. Thank you Jeremy

ADD REPLYlink written 7.2 years ago by Michael Dondrup43k

HT Sequence Analysis with R and Bioconductor seems to be a great resource and I didn't find HyperGeometericTest over there. Anyway thanks to Jeremy for his detail descritpion

ADD REPLYlink written 6.9 years ago by Thaman3.2k

+1 for Adler's R in a Nutshell which I have found to be very helpful for getting to grips with data munging especially.

ADD REPLYlink written 6.1 years ago by James Estevez90

+1 for Adler's R in a Nutshell which I have found to be very helpful for getting to grips with R, especially data munging.

ADD REPLYlink written 6.1 years ago by James Estevez90
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8
gravatar for lexnederbragt
7.2 years ago by
lexnederbragt1.2k
Oslo, Norway
lexnederbragt1.2k wrote:

Very basic, but it helped me get started, although I was mainly just interested in importing tabular data and plotting:

Zuur, Alain et al: A Beginner's Guide to R

ADD COMMENTlink written 7.2 years ago by lexnederbragt1.2k
6
gravatar for Hanif Khalak
7.2 years ago by
Hanif Khalak1.2k
Doha, QA
Hanif Khalak1.2k wrote:

Some online resources:

Quick-R a set of tutorials that I found to be to be a very lucid and practical introduction for general data analysis with R.

Data Analysis Examples at UCLA a nice matrix of various canonical analytical tasks in R as well as SAS, SPSS, etc.

R and BioConductor Manual a concise introduction to R for bioinformatics specifically

ADD COMMENTlink modified 5.2 years ago by Leonor Palmeira3.5k • written 7.2 years ago by Hanif Khalak1.2k

This is strange. Did some data get lost here on the transfer from old biostar or something?

ADD REPLYlink written 5.2 years ago by Obi Griffith15k

I think this happened while transferring but if you will click on revisions, then you can see the links.

ADD REPLYlink written 5.2 years ago by Vikas Bansal2.2k

I've edited this answer to delete the <dd> and <dt> HTML tags responsible for this. It's actually not the first time I see these [?] instead of links, so I guess this should be issued in github.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Leonor Palmeira3.5k
6
gravatar for Zach Stednick
6.9 years ago by
Zach Stednick610
Seattle, WA
Zach Stednick610 wrote:

I have R in a Nutshell on my desk and I use it at least weekly if not daily. Its well indexed with a lot of great examples and helps me save time by not searching online. The BioC chapter is decent, but quite short. I also bought Data mashups in R which I found to be a great purchase and a fun way to learn about GIS capabilities and the Yahoo API in addition to R.

ADD COMMENTlink written 6.9 years ago by Zach Stednick610
5
gravatar for Mary
6.9 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Oh, I'm glad this got bumped--just yesterday I saw a new guide to R that might be useful:

The Undergraduate Guide to R

ADD COMMENTlink written 6.9 years ago by Mary11k
5
gravatar for Obi Griffith
5.6 years ago by
Obi Griffith15k
Washington University, St Louis, USA
Obi Griffith15k wrote:

I have to give a shout out for the "R Graph Gallery". When learning to make graphs/visualizations, this resource is indispensable. Sometimes when I'm trying to think of a way to visualize some data, I just browse through the gallery for inspiration. Then, if you find something you like, all the code to get you started is right there.

http://addictedtor.free.fr/graphiques/ (now dead)

UPDATED LINKS:

ADD COMMENTlink modified 4.3 years ago • written 5.6 years ago by Obi Griffith15k

does not exist do you have any other link?

ADD REPLYlink written 4.3 years ago by Medhat6.9k

Thanks for spotting this. It seems that the excellent R graph gallery has moved. I've updated and added links to similar resources.

ADD REPLYlink written 4.3 years ago by Obi Griffith15k
4
gravatar for D. Puthier
6.9 years ago by
D. Puthier320
France/Marseille/Inserm
D. Puthier320 wrote:

SimpleR

ADD COMMENTlink written 6.9 years ago by D. Puthier320
3
gravatar for Anuraj Nayarisseri
6.0 years ago by
Indore
Anuraj Nayarisseri740 wrote:

R programming for bioinformatics By Robert Gentleman

ADD COMMENTlink modified 5.2 years ago by Leonor Palmeira3.5k • written 6.0 years ago by Anuraj Nayarisseri740
3
gravatar for Manu Prestat
5.6 years ago by
Manu Prestat3.8k
Marseille, France
Manu Prestat3.8k wrote:

About R graphics, an introduction by Paul Murrell is very popular. And, you know what? He shares all the figures code and 3 chapters via his website. It's a very good one.

ADD COMMENTlink written 5.6 years ago by Manu Prestat3.8k
3
gravatar for Malachi Griffith
5.6 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith15k wrote:

I have found these two helpful:

S Poetry by Patrick J Burns

An introduction to S and S plus by Phil Spector

ADD COMMENTlink written 5.6 years ago by Malachi Griffith15k
3
gravatar for Zev.Kronenberg
5.6 years ago by
United States
Zev.Kronenberg11k wrote:

I love plotting:

http://books.google.com/books?id=F_hwtlzPXBcC&printsec=frontcover&dq=ggplot2&hl=en&sa=X&ei=D7I1T_7oGcPmiALezJCUCg&ved=0CDIQ6AEwAA#v=onepage&q=ggplot2&f=false

ggplot is an amazing [R] package. I use it every day.

ADD COMMENTlink written 5.6 years ago by Zev.Kronenberg11k
3
gravatar for Woa
5.6 years ago by
Woa2.6k
United States
Woa2.6k wrote:

"Statistics Using R with Biological Examples" by Kim Seefeld helped me a lot

also "Applied Statistics for Bioinformatics using R" by Wim P. Krijnen

ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Woa2.6k

BTW, anyone gone through the book "Statistics and Data Analysis for Microarrays Using R and Bioconductor" by Sorin Draghici? From the Amazon preview I found it quite interesting http://www.amazon.com/Statistics-Microarrays-Bioconductor-Mathematical-Computational/dp/1439809755/

ADD REPLYlink written 5.6 years ago by Woa2.6k

I just got a copy of Draghici's book and I found it to be FANTASTIC. I will possibly buy a copy soon and look for his upcoming title "An Introduction to Statistics and Data Analysis for Bioinformatics using R" to be released in Sep 15, 2012

ADD REPLYlink written 5.6 years ago by Woa2.6k
2
gravatar for Parham
2.9 years ago by
Parham1.3k
Sweden
Parham1.3k wrote:

http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#TOC-Vectors

http://www.bioinformatics.babraham.ac.uk/training.html#rintro

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Parham1.3k
21
gravatar for Pierre
7.5 years ago by
Pierre480
Spain
Pierre480 wrote:

A comment, not answering your question but which may help a lot people using R: If you are very annoyed that it is impossible to make a google search for R, use rseek.org. It is basicly R-specific google.

ADD COMMENTlink written 7.5 years ago by Pierre480
2

googling r-project works pretty well too

ADD REPLYlink written 7.4 years ago by Heather Piwowar380

This is really cool and helpful in any way. Yes, I was annoyed searching for one character languages "C, R". Had the authors of the languages anticipated google, they might have used something like R++ ;)

ADD REPLYlink written 7.5 years ago by Michael Dondrup43k
10
gravatar for David Quigley
7.2 years ago by
David Quigley10k
San Francisco
David Quigley10k wrote:

Introductory Statistics with R by Peter Dalgaard is a wonderful, brief introduction to basic statistical practice using R. If you want to know how to perform survival analysis, specify linear models, build plots, etc. it is a very clear guide. It is not bioinformatics-specific, and does not mention Bioconductor.

In general I've found the quality of the Springer books to be very high. If you're affiliated with a large university (e.g. UCSF), you may be able to browse their texts for free from your desk through SpringerLink.

ADD COMMENTlink written 7.2 years ago by David Quigley10k

Great pick. It really helped with both statistical modeling and R programming.

ADD REPLYlink written 7.2 years ago by Hanif Khalak1.2k
6
gravatar for Ruchira
7.2 years ago by
Ruchira220
Berkeley, California
Ruchira220 wrote:

I upvoted David Quigley's recommendation of the Dalgaard book. I'd also recommend Modern Applied Statistics with S by Venables & Ripley. Despite the title, it's totally relevant to R. From the first page of the Introduction, "An Open Source system called R has emerged that provides an independent implentation of the S language. It is similar enough that almost all the examples in this book can be run under R." This book is pretty much the standard reference for R in book form.

ADD COMMENTlink written 7.2 years ago by Ruchira220

R is derived from S, or vice versa as some would argue!

ADD REPLYlink written 6.9 years ago by Larry_Parnell16k
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