package, each
component of adegenet is documented in help pages. As a starting
point, one can type ?adegenet in R to get an
overview of package. Other sources of information distributed
with the package include a manual and vignettes. This website
also provides other resources such as lectures and practicals.To search quickly through these resources, use the search engine.
Manuals
- the adegenet manual (pdf), which compiles all the manpages of the package.
Tutorials*
Up-to-date tutorials are now hosted on Github:
https://github.com/thibautjombart/adegenet/wiki/Tutorials
Lectures and practicals
- globaldiv summer school 2009, Piacenza, Italie: talk - practical course
- Master 2 "Ecology, Evolution, Biometry", Lyon, France:
talk - practical course
- One-week course on Genetic Data Analysis, Bogota, Colombia:
- lecture 1: methodological overview
- lecture 2: finding clusters, using cluster information
- lecture 3: spatial genetics
- practical 1 [version with all commands]
- practical 2 [version with all commands]
- practical 3
- MRC methodological session: Introduction to phylogenetics:
- slides
- practical
- data (DNA sequences, annotations)
- RAPID-NGS workshop, Münster (March 2013) - Outbreak analysis using ape and adegenet
- practical
- data (cases.csv,
alignment.fa,
update.csv)
- Imperial College - Master Modern Epidemiology / Public Health: Introduction to phylogenetics (last updated on the 15/13/2013)
- practical
- data (usflu.fasta, usflu.annot.csv)
- Imperial College - Master Modern Epidemiology / Public Health: Introduction to multivariate analysis / bacterial GWAS (last updated on the 21/13/2013)
- lecture
- practical
- data (simGWAS.RData)
- GenEpi workshop, London (April 2013) - Outbreak analysis using ape, adegenet, and outbreaker
- talk
- practical
- data (cases.csv,
alignment.fa,
update.csv)
- Molecular Outbreak Epidemiology workshop, Stockholm, Sweden (November 2013) - Outbreak analysis using ape, adegenet, and outbreaker
- talk
- practical
- data (cases.csv,
alignment.fa,
update.csv)
- Workshop "Phylogenetics and population genetics using R", Montpellier (March 2014)
- Multivariate analysis of genetic data: an introduction [lecture, practical]
- Multivariate analysis of genetic data: exploring group
diversity [lecture,
practical]
- Multivariate analysis of genetic data: uncovering spatial
structures [lecture,
practical]
- XXIV International Symposium of Statistics, Bogota, Colombia (July 2014) - Multivariate analysis of genetic data: an introduction for statisticians
- slides
of the lecture
- Workshop "Genetic data analysis using R" - Leuven (October 2014)
- Short R refresher [lecture]
- Introduction to phylogenetics [lecture, practical]
- Multivariate analysis of genetic data: an introduction [lecture, practical]
- Multivariate analysis of genetic data: exploring group diversity [lecture, practical, practical all commands]
- An introduction to Genome Wise Association Studies (GWAS) [lecture, practical]
- Multivariate analysis of genetic data: uncovering spatial structures [lecture, practical]
- Workshop "Genetic data analysis with R" - Glasgow (August 2015)
- Introduction to phylogenetics [lecture, practical]
- Multivariate analysis of genetic data: an introduction [lecture, practical]
- Multivariate analysis of genetic data: exploring group
diversity [lecture,
practical]
- An introduction to Genome Wise Association Studies (GWAS)
[lecture,
practical,
data]
- Multivariate analysis of genetic data: uncovering spatial
structures [lecture,
practical]
- Workshop "Exploratory methods for population genetics using R" - Barcelona (October 2015)
- Multivariate analysis of genetic data: an introduction [lecture, practical]
- Multivariate analysis of genetic data: exploring group
diversity [lecture,
practical]
- Multivariate analysis of genetic data: uncovering spatial
structures [lecture,
practical]
- Workshop "Genetic data
analysis with R" - Cumbrae (August 2016)
- Introduction to phylogenetics [lecture, practical]
- R refresher [lecture]
- Multivariate analysis of genetic data: an introduction [lecture, practical]
- Multivariate analysis of genetic data: exploring group diversity [lecture, practical, practical with all commands]
- Multivariate analysis of genetic data: uncovering spatial structures [lecture, practical]
- Reproducible science using R [lecture, foo.Rmd, bar.Rnw]
- Workshop "Population genomics using R" - Lausanne
(August 2016)
- a small hack for installing R packages on computers without administrative rights: hackLib.R README
Mailing lists archives
Use the search engine to browse the archives of the adegenet forum.
See the 'contact' section of this website for further information on mailing lists.