sirselim/methylation_EWAS_workshop

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sirselim/methylation_EWAS_workshop

sirselim

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This is a basic EWAS tutorial, introducing basic concepts for analysing methylation data

jetson_nanopore_sequencing

A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.

guppy_parameter_optimiser

A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate

illumina450k_filtering

A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays

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

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.

GPU-musings

A collection of my thoughts around GPUs for genomic analysis and sequencing

presentation_and_design_resources

A small repo to hold useful resources for various courses I teach

sirselim.github.io

Personal website, blog and notebook

VCF-DART_example_exomes

A few example exomes in vcf format for testing the VCF-DART annotation and reporting tool

tSNE_plotting

some documentation for exploring the plotting of tSNE results from various data sources

lyritical

Analysis of song and artist lyrics in R - just for fun!!

singularity-genmod

A quick singularity recipe for genmod to facilitate use in variant annotation pipelines

cpg_annotate

small R script to provide quick annotation and gene lists for series of IlmnID's (450k probes)

vega-lite_integration_testing

A basic repository housing files detailing R and Python integration testing of vega-lite graphics

R_notebooks

A quick overview of using R Notebooks as a form of electronic lab book for bioinformatics

presentation_learnings_from_NI

My presentation for the AGTA 2016 conference to be held in Auckland (Oct 9-12th, 2016)

NvidiaGTC_2021

My 40min presentation for Nvidia Spring GTC 2021 on portable sequencing tech and Nvidia GPUs

Introduction-to-R-and-RStudio

An introductory overview of R and the fantastic IDE RStudio - rendered in Gitbook format

sirselim

autosomal_markers

Bookdown_Lab_Notebook

Testing bookdown as an electronic lab book option

data_carpentry_notes

Notes made available for various data carpentry sessions