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R and Bioconductor Tutorial
By Jitendra Narayan 4111 days ago Comments (63)
http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual
This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that biologists need to perform some basic analysis: load a table, plot some graphs, and perform some basic statistics. More extensive tutorials can be found on the project website and via bioconductor (not covered here).
You can add more tutorial links in comments if found new pages.
Comments
A self learning R tutorial at http://www.nceas.ucsb.edu/files/scicomp/Dloads/RProgramming/BestFirstRTutorial.pdf
Rattle: A Graphical User Interface for Data Mining using R http://rattle.togaware.com/
IDE for R http://www.rstudio.com/ide/
It is available in open source and commercial editions and runs on the desktop (Windows, Mac, and Linux) or over the web with RStudio Server.
A web application framework for R. http://shiny.rstudio.com/ It turn your analyses into interactive web applications. No HTML, CSS, or JavaScript knowledge required :)
Yet another useful R tutorial at http://www.nceas.ucsb.edu/files/scicomp/Dloads/RProgramming/BestFirstRTutorial.pdf
Resources to help you learn and use R http://www.ats.ucla.edu/stat/r/
Sean Davis tutorial is really useful http://watson.nci.nih.gov/~sdavis/tutorials/
Little Book of R for Bioinformatics by Avril Coghlan, Wellcome Trust Sanger Institute, Cambridge, U.K. http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/
APE: Analyses of Phylogenetics and Evolution in R language http://bioinformatics.oxfordjournals.org/content/20/2/289.abstract
R for Bioinformatics http://www.evolution.unibas.ch/teaching/evol_genetics/1_Bioinformatics/lecture_notes/HS2013_9_R.pdf
R tutorial stuff at http://math.illinoisstate.edu/dhkim/rstuff/rtutor.html
R/parallel – speeding up bioinformatics analysis with R http://www.biomedcentral.com/1471-2105/9/390
NetWorkSpaces for R http://nws-r.sourceforge.net/
Next generation sequencing data analysis with R/Bioconductor http://www.bioconductor.org/help/course-materials/2012/CSC2012/Bioconductor-tutorial.pdf
NGS with R
More at https://rc.fas.harvard.edu/kb/bioinformatics/sequencing-information/ngs-analysis-with-r/
http://bioconductor.org/help/workflows/high-throughput-sequencing/
A self learn R tutorial at http://www.nceas.ucsb.edu/files/scicomp/Dloads/RProgramming/BestFirstRTutorial.pdf
R and Bioconductor for NGS data analysis http://master.bioconductor.org/help/course-materials/2012/CSC2012/Bioconductor-tutorial.pdf
http://manuals.bioinformatics.ucr.edu/home/ht-seq
Generate map with R http://students.washington.edu/bowmanjs/wordpress/?p=1003
Phylogenetic capabilities in R http://www.r-bloggers.com/phylogenies-in-r-and-python/
A quick tutorial on R https://github.com/jrherr/quick_basic_R_tutorial/blob/master/basic_R_tutorial.R
Little book of R for Bioinformatics http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter9.html
On DataCamp.com you can find free interactive courses on data science and R (similar to tryR by code school but a lot more focused) :
> Introduction to R course https://www.datacamp.com/courses/introduction-to-r
> Data analysis and statistical inference course by a professor from Duke University https://www.datacamp.com/courses/data-analysis-and-statistical-inference_mine-cetinkaya-rundel-by-datacamp
> Computational finance https://www.datacamp.com/courses/introduction-to-computational-finance-and-financial-econometrics
New courses in collaboration with RStudio and Revolution analytics are on the way. Just like a new course on statistics with R (together with a professor from Princeton University), and a course focused on R for SAS users.
This tutorial is good for beginners http://evolution.unibas.ch/teaching/evol_genetics/1_Bioinformatics/lecture_notes/HS2013_9_R.pdf
There are several R packages to use image data for statistical analysis and modeling
EBImage
http://master.bioconductor.org/help/course-materials/2010/CSAMA10/100617-pau-brixen-ebimage-2.pdf
http://www.bioconductor.org/packages/release/bioc/html/EBImage.html
http://www.bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/doc/EBImage-introduction.pdf
EMBL tutorial
http://www.bioconductor.org/help/course-materials/2010/BioC2010/100730-seattle-huber.pdf
http://www.maths.usyd.edu.au/u/jeany/Papers/springer02.pdf
Tableau (statistical horsepower of R with user-friendly visual analytics)
http://www.tableausoftware.com