There is a wealth of well written and high quality teaching resources available online. The purpose of this page is two fold.

  • Firstly to direct students on courses I teach to course specific materials. Although the course specific stuff can also found in the University of Dundee myDundee VLE system I a making it available here.
  • Secondly to provide links to resources I find useful myself.

Undergraduate

BS32010 Applied Bioinformatics   Resources for Microarray and RNAseq workshops for BSc Bioinformatics


Post-graduate

RNA-seq with R/Bioconductor   Resources for the workshops that are part of the Data Analysis Group post-grad/doc teaching series


Encode

ENCODE tools  Various tools for accessing and analysing ENCODE data
ENCODE example  An example using rtracklayer and GenomicRanges for a very simple analyse of an ENCODE data


Useful R/bioconductor

R Documentation  R Docuemtation project
Packages Tutorial  A useful tutorial on git hub for writing packages in R
Packages Book  Hadley Wickhams R packages online book
Advanced R Book  Hadley Wickhams Advanced R online book
Documentating With roxygen  Hadley Wickhams vignettes for his roxygen2 package
R-Style Guide Guide to writing well formated R also has linkes to other Guides
UC Riverside REALLY USEFUL SITE A lot of useful information on using R and Bioconductor but also Linux, Galaxy and IGV


Other Resources

knitr package Website for the R package knitr for producing documentation with embedded code
rmarkdown package Website for the R package rmarkdown nice and easy way to produce literate programming documents
Reproducible Research  Link to a CRAN page on reproducible research resources in R
Literate programming  Wikipedia description of the aims of literate programming “The main idea is to regard a program as a communication to human beings rather than as a set of instructions to a computer.” Knuth.