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index.Rmd
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---
title: "Nicholas Eagles"
image: "nick.jpg"
links:
- label: LinkedIn
url: "https://www.linkedin.com/in/nick-eagles-7a5b30161/"
- label: GitHub
url: "https://github.com/Nick-Eagles"
- label: Email
url: "mailto:[email protected]"
output:
postcards::trestles
---
## Bio
I'm currently a Research Associate in the [data science team](https://lcolladotor.github.io/bioc_team_ds/) led by Leonardo Collado-Torres at [LIBD](https://www.libd.org/).
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](https://doi.org/10.1186/s12859-021-04142-3)), whole-genome bisulfite sequencing (see [BiocMAP](https://doi.org/10.1101/2022.04.20.488947)), spatial transcriptomics (see [visiumStitched](https://doi.org/10.1186/s12864-024-10991-y)), and cell-type deconvolution.
I also help [install and maintain software](https://github.com/LieberInstitute/jhpce_mod_source) for LIBD and collaborators, and mentor and share my knowledge through [data science guidance sessions](https://lcolladotor.github.io/bioc_team_ds/data-science-guidance-sessions.html) and [R Stats Club](http://research.libd.org/rstatsclub/) presentations. Some example topics I've taught include [implementing machine-learning models in python](https://youtu.be/-qFz7PwWEeY), [system-wide software installations on high-performance computing clusters with Lmod](https://youtu.be/8w6JDsrgqVs), and [running PyTorch-based software with GPUs at HPC environments](https://youtu.be/zOMUXYHtVJM).
## 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](https://doi.org/10.1186/s12864-024-10991-y)
- Eagles et al., *BMC Genomics*, 2024.
[BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data](https://doi.org/10.1186/s12859-023-05461-3)
- Eagles et al., *BMC Bioinformatics*, 2023.
[SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.](https://doi.org/10.1186/s12859-021-04142-3)
- Eagles et al., *BMC Bioinformatics*, 2021.
My full list of publications is available at my [ORCID profile](https://orcid.org/0000-0002-9808-5254).
## Public Presentations
**Bioconductor** | *Bioconductor* | 2023
- Presented a workshop: [A Bioconductor-style differential expression analysis powered by SPEAQeasy](http://research.libd.org/SPEAQeasyWorkshop2023/) recorded as a [video](https://www.youtube.com/watch?v=6hJXPw9PM1o)
- Presented a short talk: [Spot Deconvolution in the Post-Mortem Human DLPFC](https://speakerdeck.com/nickeagles/bioc-2023-spot-deconvolution) recorded as a [video](https://www.youtube.com/watch?v=YA5H2XP6jjU&t=700s)
**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](https://speakerdeck.com/nickeagles/bds-2022).
**European Bioconductor** | *Bioconductor* | 2020
- Presented my [SPEAQeasy paper](https://www.youtube.com/watch?v=tPSG23hUHSI).