Devon Allies

I’m a bioinformatician and computational biologist with over 15 years in biomedical science, including 10 in tuberculosis research. I started at the lab bench, processing clinical samples and running flow cytometry, went on to coordinate multi-site clinical studies, and now build the pipelines and analyses that turn genomic and clinical data into results. I’m currently a Data Analyst at Stellenbosch University and completing an MSc in Computational Biology.

View projects About me

15+ years in biomedical science

3 peer-reviewed papers

100+ citations

8 portfolio projects

Featured projects

A Nextflow Pipeline for Whole-Genome Variant Calling

Bioinformatics

Data engineering

Nextflow

A modular Nextflow DSL2 pipeline that takes paired-end whole-genome sequencing reads to joint-called, filtered variants with BWA-MEM, SAMtools and GATK, built to run on a…

Credit Risk Pipeline on Databricks

A bronze/silver/gold lakehouse pipeline on Databricks that cleans messy lending data, builds a leakage-free loan table and trains MLflow-tracked default models, with a…

Databricks Data Pipeline: Simulated BAL Study

Bronze, silver and gold Delta tables, tested cleaning functions, MLflow model tracking and a Streamlit demo, built on simulated clinical data.

Differential Expression Analysis of Chromosome X RNA-seq Data

Bioinformatics

Statistics

Sex-based differential expression on chromosome X from 12 paired-end RNA-seq samples, using a Nextflow pipeline with HISAT2 and StringTie, and Ballgown in R.

Latest

Tutorial

Using one dataset in both R and Python

Tutorial 2

Use reticulate to turn an R data frame into a pandas DataFrame and back, so R and Python can work on the…

Article

Enhancing Reproducibility: A Deep Dive into My Updated Quarto Scientific Writing Template

Medium · 04 June 2025

In May, I wrote an article detailing my switch to RStudio® for scientific writing. I also introduced the concept of reproducibility, mentioning…

Paper

Optimising the yield from bronchoalveolar lavage on human participants in infectious disease immunology research

Scientific Reports · 2023

Co-authored, cited 10 times. All publications →

Get in touch

I’m always happy to talk about bioinformatics, data science and TB research.

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