boboppie/TeachingMaterial

Various teaching material

TeachingMaterial

This repository is an aggregator for various R, make and git/github teaching material. Most of the courses are taught at the University of Cambridge, UK, and some have been adapted and exported outside. We would also like to acknowledge contributions from Aleksandra Pawlik, Software Sustainability Institute, Raphael Gottardo, Fred Hutchinson Cancer Research Center and Karl Broman, University of Wisconsin-Madison.

Each material subdirectory has its own repository; TeachingMaterial aggregates a snapshot as a central entry point. Aggregation is done using git-subtree (see the administration page for details). The local copies linking to external repositories are prefixed with an underscore.

Unless otherwise stated, all material is licensed under a Creative Commons Attribution-ShareAlike 3.0 License. This means you are free to copy, distribute and transmit the work, adapt it to your needs as long as you cite its origin and, if you do redistribute it, do so under the same license.

See also the TeachingMaterial wiki for meta-information about the repository and general R installation material and links.

If you like this material and/or this initiative, do not hesitate to let us know by starring the repo, tweeting about it and sharing it with your colleagues.

Material

rbc

• Description: Software carpentry R bootcamp, Jan 7-8, 2014, Cambridge, UK and 6-7 Nov 2014, Zurich, Switzerland.
• Authors: Stephen Eglen, Laurent Gatto, Robert Stojnić and Aleksandra Pawlik
• Original repository: https://github.com/lgatto/rbc/
• Content: R programming, plotting, git/github (via software carpentry), make, shell and knitr, profiling, testing, debugging.

spr

• Description: Scientific Programming with R, MPhil in Computational Biology
• Author: Stephen Eglen with contributions from Laurent Gatto
• Original repository: https://github.com/lgatto/spr
• More details: https://github.com/lgatto/spr#readme

Biostat-578

• Description: Bioinformatics for Big Omics Data
• Author: Raphael Gottardo, Fred Hutchinson Cancer Research Center
• Original repository: https://github.com/raphg/Biostat-578
• More details: https://github.com/raphg/Biostat-578/blob/master/README.md

rbioc-proteomics

• Using R/Bioconductor for MS-based proteomics data analysis
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/rbioc-proteomics
• More details: https://github.com/lgatto/rbioc-proteomics#readme

github_tutorial

• Description: git/github guide
• Original repository: https://github.com/kbroman/github_tutorial
• Author: Karl Broman, University of Wisconsin-Madison
• View it here: http://kbroman.github.io/github_tutorial/

minimal_make

• Description: minimal tutorial on make
• Original repository: https://github.com/kbroman/minimal_make
• Author: Karl Broman, University of Wisconsin-Madison
• View it here: http://kbroman.github.io/minimal_make/

QuickPackage

• Description: Two brief overviews of R package creation
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/QuickPackage
• More details: https://github.com/lgatto/QuickPackage#readme
• Download the QuickPackage and QuickPackageAndMore slides (pdf)

R package development

• Description: Developing, documenting and testing an R package
• Author: Laurent Gatto and Robert Stojnić
• Original repository: https://github.com/lgatto/RPackageDevelopment
• More details: https://github.com/lgatto/RPackageDevelopment#readme
• Download the pdf

Benchmarking, profiling and optimisation

• Description: Benchmarking, profiling and optimisation
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/R-bmark-prof-optim
• More details: https://github.com/lgatto/R-bmark-prof-optim#readme
• Read the material

RBasics

• Description: A introduction to R for knowledgeable bioinformaticians. Used as R intro lecture for the CSAMA workshop.
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/RBasics
• More details: https://github.com/lgatto/RBasics#readme
• Download the pdf

RIntro

• Description: A 1 day introductionary course, developed specifically for Microarray Analysis using R and Bioconductor.
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/RIntro
• More details: https://github.com/lgatto/RIntro#readme
• Download the pdf

basicr

• Description: Material for the 2-day R introduction taught at Cambridge's Graduate School of Life Sciences Training.
• Authors: Robert Stojnic, Laurent Gatto, Rob Foy, David Molnar and John Davey, based on original slides by Ian Roberts and Robert Stojnic.
• Original repository: https://github.com/johnomics/basicr/
• Course page: http://logic.sysbiol.cam.ac.uk/teaching/Rcourse/
• Download the slides for day 1 and day 2 in pdf.

R functional programming

• Description: A short topic section on functional programming in R
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/R-functional-programming
• More details: https://github.com/lgatto/R-functional-programming#readme
• Download the pdf

R vectorisation

• Description: A short topic section on vectorisation in R
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/R-vectorisation
• More details: https://github.com/lgatto/R-vectorisation#readme
• Download the pdf

R debugging

• Description: A short topic section on debugging in R
• Author: Laurent Gatto and Robert Stojnić
• Original repository: https://github.com/lgatto/R-debugging
• More details: https://github.com/lgatto/R-debugging#readme
• Download the pdf

R parallel

• Description: A short topic section on parallal computing in R
• Author: Laurent Gatto and Robert Stojnić
• Original repository: https://github.com/lgatto/R-parallel
• More details: https://github.com/lgatto/R-parallel#readme
• Download the pdf

R object oriented programming

• Description: Covers S3, S4 and S4 Reference Classes OO programming using DNA/RNA sequence data manipulation as a working example.
• Author: Laurent Gatto and Robert Stojnić
• Original repository: https://github.com/lgatto/roo
• More details: https://github.com/lgatto/roo#readme
• Download the pdf

Short S4 tutorial

• Description: A practical S4 object-oriented programming tutorial using microarrays as a working example.
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/S4-tutorial
• More details: https://github.com/lgatto/S4-tutorial#readme
• Download the pdf

R programming tutorial

• Description: A tutorial on R programming of intermediate level, focusing on some aspects of functional programming, profiling, testing, debugging and parallelisation. Used as more advanced R programming lecture during the CSAMA workshop.
• Author: Laurent Gatto
• Original repository: https://github.com/lgatto/R-programming
• More details: https://github.com/lgatto/R-programming#readme
• Download the pdf

R and C/C++

• Description: Writing and calling C/C++ code for/from R
• Author: Laurent Gatto
• Many examples from the Rcpp gallery and from Dirk's slides.
• Original repository: https://github.com/lgatto/rccpp
• More details: https://github.com/lgatto/rccpp#readme
• Download the pdf

visualisation

• Description: visualising data using ggplot2 (more to come soon)
• Author: Mark Dunning
• Original repository: https://github.com/lgatto/visualisation
• Download the pdf

sequences

• Description: Educational package used in R to illustrate OO programming and package development
• Author: Laurent Gatto and Robert Stojnić
• Original repository: https://github.com/lgatto/sequences
• More details: https://github.com/lgatto/sequences/blob/master/DESCRIPTION
• Installation from CRAN: install.packages("sequences")
• Installation from github (requires R and C/C++ building tools):

library(devtools)
install_github("sequences", "lgatto")