duncanmr Goto Github PK

.doom.d

dotfiles

Bare repository of my dotfiles

geneticinheritancegraph

pedigrees_project

Developing methods to identify pedigree structure in tree sequence data created from Whole Genome Sequencing samples. Part of my rotation project with Dr Jerome Kelleher's lab at the Big Data Insitute, University of Oxford.

snakemake_tutorial

Solution to a Snakemake NGS pipeline tutorial

tda-for-cxr

Functions for producing topological features from lung x-ray images.

tsinfer-qc

Utilities for evaluating tsinfer inferences

tskit

Population-scale genomics

vcf-prioritise

Nextflow pipeline for annotating and prioritising variants from Whole Genome Sequencing data

vpot-nf

VPOT - Variant Prioritisation Ordering Tool. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files. Modified with an additional function to divide variants with multiple gene panels.

wgs-variant-analysis

This repository includes all the code and shell commands I used to analyse six Whole Genoming Sequencing (WGS) samples as part of Bioinformatics Master's project at Stellenbosch University, South Africa. The goal of my project is to find medically relevant variants and compile them in a report for the patient's clinician.Ethics approval was obtained for the study, however the patient data can obviously not be shared publically.