Below is a collection of vignettes I have made over the years. My general goal is to try create one vignette per first author paper, in it capturing some aspect of the data processing or analysis that I had to learn for the project. My aim in creating these is is threefold:
- increase my research repeatability and transparancy
- provide a starting point for other researches who need help with the code
- reflect on new program/techniques learnt duing projects and note areas of improvment for the future
I do not imagine these vignettes are free from errors, however if you spot any major ones or would just like general assistance with anything feel free to contact me.
SNP variant calling
Calling SNPs from raw DArTseq data using a few mapping and variant calling softwares.
Distribution Map
Retrieving data from eBird and using it to plot a species distribution map.
Full workshops have been developed for:
- Redundancy Analysis: Ecology and multivariate statistics covering redundancy analysis of cane toad phenotype data.
- Genetic Outlier Analysis: Covering the basics of PCAdapt, Fst, BayeScan, and BayPass, and some discussion around selection analysis on genomic data. Another version of this workshop is available through GenomicsAotearoa, which has been updated to run on New Zealand eScience Infrastructure (NeSI).
In addition to this, I like running discussion groups about how to construct thesis chapters and manuscripts. Some of the notes on this can be found here.