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.
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.
- Description: Software carpentry R bootcamp, Jan 7-8, 2014, Cambridge, UK
- Authors: Stephen Eglen, Laurent Gatto and Aleksandra Pawlik
- Original repository: https://github.com/lgatto/rbc/
- Content:
R
programming, plotting,git
/github
(via software carpentry),make
,shell
andknitr
.
- Description: Scientific Programmign 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
- 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
- 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/
- 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/
- Description: Twobrief 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)
- 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
- Description: A introduction to
R
for knowledgeable bioinformaticians. Used asR
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
- 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
- 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.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Description: Writing and calling
C
/C++
code for/fromR
- 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
- Description: visualising data using
ggplot2
(more to come soon) - Author: Mark Dunning
- Original repository: https://github.com/lgatto/visualisation
- Download the pdf
- 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
andC/C++
building tools):
library(devtools)
install_github("sequences", "lgatto")