BOL: R and Bioconductor Tutorial

R and Bioconductor Tutorial

Jitendra Narayan — Fri, 23 Aug 2013 08:23:59 -0500

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.

Address of the bookmark: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual

Comment by Abhimanyu Singh

Abhimanyu Singh — Tue, 30 Oct 2018 10:21:48 -0500

R graphics https://bioconductor.org/packages/devel/bioc/vignettes/chromPlot/inst/doc/chromPlot.pdf #chromPlot

Comment by Gudiya Pal

Gudiya Pal — Fri, 01 Jul 2016 11:11:18 -0500

Colour in R http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf

Comment by Jit

Jit — Thu, 30 Jun 2016 08:38:48 -0500

A Compendium of Clean Graphs in R http://shinyapps.org/apps/RGraphCompendium/index.php

Comment by Jit

Jit — Fri, 24 Jun 2016 19:46:43 -0500

R tutorial for bioinformatician http://www.introductoryr.co.uk/R_Resources_for_Beginners.html

Comment by Rahul Nayak

Rahul Nayak — Fri, 29 Apr 2016 15:15:19 -0500

Learn R by urself www.datasciencecentral.com/profiles/blogs/learning-r-in-seven-simple-steps

Comment by Nishi Singh

Nishi Singh — Sat, 07 Nov 2015 07:43:15 -0600

Useful R resource http://ucanalytics.com/blogs/r-vs-python-comparison-and-awsome-books-free-pdfs-to-learn-them/

Comment by Jitendra Prajapati

Jitendra Prajapati — Sat, 29 Aug 2015 08:13:50 -0500

There are many othe useful turoial on R package creation, such as

http://www.r-bloggers.com/creating-an-r-package-in-windows/

http://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

http://www.r-bloggers.com/how-to-create-an-r-package-in-windows/

Comment by Aasha

Aasha — Sat, 29 Aug 2015 07:57:52 -0500

R package development https://www.rstudio.com/products/rpackages/devtools/

Comment by Jitendra Narayan

Jitendra Narayan — Sat, 29 Aug 2015 06:35:17 -0500

Create the R package https://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf

Comment by Rahul Nayak

Rahul Nayak — Sun, 21 Jun 2015 21:03:01 -0500

Reading Genomics Data into R/Bioconductor http://bcb.dfci.harvard.edu/~aedin/courses/Bioconductor/3.ReadWrite.pdf

Comment by Rahul Nayak

Rahul Nayak — Sun, 21 Jun 2015 18:24:32 -0500

Welcome to a Little Book of R for Bioinformatics http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/

Comment by Rahul Nayak

Rahul Nayak — Sun, 21 Jun 2015 18:20:23 -0500

Genes and genome with R https://www.ebi.ac.uk/training/sites/ebi.ac.uk.training/files/materials/2013/131021_HTS/genesandgenomes.pdf

Comment by Robert M Willioms

Robert M Willioms — Wed, 10 Sep 2014 14:46:37 -0500

R for epigenetics http://www.bristol.ac.uk/caite/geocode/newcastleshortcourse/bioinformaticstoolsforepigen.pdf

Comment by Rahul Agarwal

Rahul Agarwal — Sun, 07 Sep 2014 03:17:50 -0500

Tableau (statistical horsepower of R with user-friendly visual analytics)

http://www.tableausoftware.com

Comment by Jit

Jit — Sun, 07 Sep 2014 00:04:31 -0500

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

Comment by Jitendra Narayan

Jitendra Narayan — Fri, 05 Sep 2014 23:30:07 -0500

This tutorial is good for beginners http://evolution.unibas.ch/teaching/evol_genetics/1_Bioinformatics/lecture_notes/HS2013_9_R.pdf

Comment by martijn theuwissen

martijn theuwissen — Wed, 13 Aug 2014 01:14:19 -0500

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.

Comment by Jitendra Narayan

Jitendra Narayan — Wed, 25 Jun 2014 10:03:03 -0500

Little book of R for Bioinformatics http://a-little-book-of-r-for-bioinformatics.readthedocs.org/en/latest/src/chapter9.html

Comment by Jit

Jit — Fri, 20 Jun 2014 03:30:43 -0500

A quick tutorial on R https://github.com/jrherr/quick_basic_R_tutorial/blob/master/basic_R_tutorial.R

Comment by Surabhi Chaudhary

Surabhi Chaudhary — Mon, 09 Jun 2014 13:24:06 -0500

Phylogenetic capabilities in R http://www.r-bloggers.com/phylogenies-in-r-and-python/

Comment by John Parker

John Parker — Wed, 04 Jun 2014 07:27:10 -0500

Generate map with R http://students.washington.edu/bowmanjs/wordpress/?p=1003

Comment by Radha Agarkar

Radha Agarkar — Mon, 12 May 2014 06:34:16 -0500

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

Comment by Archana Malhotra

Archana Malhotra — Mon, 28 Apr 2014 10:24:50 -0500

A self learn R tutorial at http://www.nceas.ucsb.edu/files/scicomp/Dloads/RProgramming/BestFirstRTutorial.pdf

Comment by Jit

Jit — Fri, 18 Apr 2014 03:44:15 -0500

NGS with R

ShortRead – Quality assesment of the reads, finding duplicates, trimming, string pattern searches [1]
Biostrings – Reading sequences in R [2]
BSGenomes – Reading in complete genomes and BioC annotation data [3]
DEGSeq – Identify differentially expressed genes from RNA-Seq data. [4]
IRanges – infrastructure for positional data.
biomaRt – interface to BioMart annotations.
rtracklayer – interface to online and other genome browsers.
chipseq & ChIPpeakAnno – Chip-Seq

More at https://rc.fas.harvard.edu/kb/bioinformatics/sequencing-information/ngs-analysis-with-r/

http://bioconductor.org/help/workflows/high-throughput-sequencing/

Comment by Jit

Jit — Fri, 18 Apr 2014 03:40:25 -0500

Next generation sequencing data analysis with R/Bioconductor http://www.bioconductor.org/help/course-materials/2012/CSC2012/Bioconductor-tutorial.pdf