Miles

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

Intro_to_GWAS. An introductory workshop to GWAS analysis using PLINK and R

diagnostics_exome_reporting. Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.

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

GPU-musings. A collection of my thoughts around GPUs for genomic analysis and sequencing

electronic_lab_notebook. This is an example of using blogdown, hugo and netlify to create and serve an electronic lab notebook.

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

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

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

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

sirselim.github.io. Personal website, blog and notebook

NvidiaGTC_2021. My 40min presentation for Nvidia Spring GTC 2021 on portable sequencing tech and Nvidia GPUs

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

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

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

mitofish. This script generates "baited" sequences from across a provided reference to search for them in fastq file(s)

Bookdown_Lab_Notebook. Testing bookdown as an electronic lab book option

data_carpentry_notes. Notes made available for various data carpentry sessions

git-collaboration. A repository to demonstrate collaboration workflows

MTG-Markdown-Generator. A Python script to generate markdown tables for Magic: The Gathering cards using the Scryfall API.

shell-genomics. Python

smrnaseq. A small-RNA sequencing analysis pipeline

sirselim.

immunecell_methylation_paper_data. This repository contains data, results and supplementary information to go alongside our manuscript detailing the validation of immune cell specific methylation markers.

MTGCardFinder. MTG Card Markdown Toolkit - a VSCode extension to grab card image and information for markdown documents.

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

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

autosomal_markers.