Bio

I’m currently a Research Associate in the data science team led by Leonardo Collado-Torres at LIBD.

Here, I use R, python, shell scripting, and more to develop computational pipelines for processing genomic data, explore and implement machine-learning methods, and publish research papers showcasing this software and biological findings. My work in genomics spans topics such as bulk-RNA-sequencing (for which I published SPEAQeasy), whole-genome bisulfite sequencing (see BiocMAP), spatial transcriptomics (see visiumStitched), and cell-type deconvolution.

I also help install and maintain software for LIBD and collaborators, and mentor and share my knowledge through data science guidance sessions and R Stats Club presentations. Some example topics I’ve taught include implementing machine-learning models in python, system-wide software installations on high-performance computing clusters with Lmod, and running PyTorch-based software with GPUs at HPC environments.

Education

University of Maryland, Baltimore County | Baltimore, MD

B.S. in Mathematics | September 2013 - May 2018

Experience

Lieber Institute for Brain Development | Research Associate II- Data Science | November 2018 - Present

Publications

Integrating gene expression and imaging data across Visium capture areas with visiumStitched

• Eagles et al., BMC Genomics, 2024.

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data

• Eagles et al., BMC Bioinformatics, 2023.

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.

• Eagles et al., BMC Bioinformatics, 2021.

My full list of publications is available at my ORCID profile.

Public Presentations

Bioconductor | Bioconductor | 2023

• Presented a workshop: A Bioconductor-style differential expression analysis powered by SPEAQeasy recorded as a video

• Presented a short talk: Spot Deconvolution in the Post-Mortem Human DLPFC recorded as a video

Biological Data Science | Cold Spring Harbor Laboratory | 2022

• Presented a poster: Benchmarking spot-level cell-type deconvolution methods using Visium immunofluorescence benchmark data on the human dorsolateral prefrontal cortex.

European Bioconductor | Bioconductor | 2020

• Presented my SPEAQeasy paper.