Miles's repositories
diagnostics_exome_reporting
Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.
Intro_to_GWAS
An introductory workshop to GWAS analysis using PLINK and R
methylation_EWAS_workshop
This is a basic EWAS tutorial, introducing basic concepts for analysing methylation data
WES_ShinyDiscover
A Shiny interface to filter and identify variants of interest from whole exome data
electronic_lab_notebook
This is an example of using blogdown, hugo and netlify to create and serve an electronic lab notebook.
cpg_annotate
small R script to provide quick annotation and gene lists for series of IlmnID's (450k probes)
VCF-DART_example_exomes
A few example exomes in vcf format for testing the VCF-DART annotation and reporting tool
vega-lite_integration_testing
A basic repository housing files detailing R and Python integration testing of vega-lite graphics
Bookdown_Lab_Notebook
Testing bookdown as an electronic lab book option
data_carpentry_notes
Notes made available for various data carpentry sessions
Introduction-to-R-and-RStudio
An introductory overview of R and the fantastic IDE RStudio - rendered in Gitbook format
presentation_learnings_from_NI
My presentation for the AGTA 2016 conference to be held in Auckland (Oct 9-12th, 2016)
R_notebooks
A quick overview of using R Notebooks as a form of electronic lab book for bioinformatics
Blog
This repository contains codes for all of my blog posts since March 11 2015.
lessons
Teaching materials used by the Research Bazaar
migraine_gene_lists
This repository curates and maintains a set of epilepsy 'related' genes in ranked tiers (biological priors)
Rgitbook
Gitbook for R Markdown
sampling-game
The player is prompted to guess the required sample size to detect loss in a population
SING_Aotearoa_2018
Basic bioinformatics workshop for SING Aotearoa 2018 exploring population genetics and epigenetics
test_teams_link
A quick test to see if we can link GitHub content 'nicely' in MS Teams.
wes_gene_lists
A curated list of genes used in the filtering steps of exome sequencing pipelines.