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Nick Eagles

@nick-eagles.bsky.social
69 followers 8 following 8 posts

Research Associate II, Data Science at Lieber Institute for Brain Development (@lieberinstitute.bsky.social) nick-eagles.github.io

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Nick Eagles @nick-eagles.bsky.social · 27/01/2026
A colleague Geo @geopertea.bsky.social found out a cool trick to get Positron working with full support at our computing cluster JHPCE (remote file explorer, Positron assistant seeing the remote R session). Game changer for my work at LIBD! Check out his demo video (youtu.be/CnmaJG8VPp8) #positron
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Nick Eagles @nick-eagles.bsky.social · 16/01/2026
Lots has evolved since these R Stats sessions @libdrstats.bsky.social, but we touch on the hot topic of integrating LLMs into data science, mostly with Github Copilot, in a couple sessions-- Introductory look: youtu.be/xuCQZ5_5KB0 Reusable prompts: youtu.be/mlMl81xRI_M #RStats #LLMs
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Nick Eagles @nick-eagles.bsky.social · 08/01/2026
In a recent journal club, I covered the SOFA paper by @wkhuber.bsky.social and colleagues. It's especially cool how you can guide the factorization approach with known covariates. Check out their preprint (doi.org/10.1101/2024...) and our discussion (youtu.be/WKs-g4lXzZs)!
doi.org
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Nick Eagles @nick-eagles.bsky.social · 13/11/2025
Hot take: ggplot2 is better than any plotting option available in Python-- but I discuss a couple options in Python at an R Stats Club session @libdrstats.bsky.social linked below. I personally use plotnine, since it's essentially a port of ggplot2 for Python. youtu.be/xK9UNcOfjnI
youtu.be
[2025-07-18] Plots in Python with seaborn and plotnine
YouTube video by Leonardo Collado Torres
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Nick Eagles @nick-eagles.bsky.social · 04/11/2025
We recently checked out tidySingleCellExperiment at the R Stats Club @libdrstats.bsky.social, an R package part of a broader effort to bring tidy coding to genomics. Pretty useful! youtu.be/ob_SQY4-YjQ?... #RStats
youtu.be
[2025-07-11] Tidy manipulation of SingleCellExperiment objects
YouTube video by Leonardo Collado Torres
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Nick Eagles @nick-eagles.bsky.social · 13/06/2025
Just covered the data.table and dtplyr packages at LIBD R Stats Club @libdrstats.bsky.social. Really useful to be able to write dplyr code and get data.table performance! #rstats youtu.be/D3u64PMlJSI
youtu.be
[2025-06-13] Intro to data.table and dtplyr for data manipulation
YouTube video by Leonardo Collado Torres
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Nick Eagles @nick-eagles.bsky.social · 06/06/2025
Do a lot of PCA? Interested in streamlining data wrangling? In a couple recent LIBD R Stats Club @libdrstats.bsky.social sessions I talk about PCAtools, and dplyr for beginners. youtu.be/rClA0Ms-oOw youtu.be/XIbraIgPt0M #RStats
youtu.be
[2025-05-23] Introduction to dplyr for data manipulation
YouTube video by Leonardo Collado Torres
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Nick Eagles @nick-eagles.bsky.social · 23/05/2025
Check out my LIBD @lieberinstitute.bsky.social R Stats Club #rstats presentation on SLURM array jobs for efficient parallel data analysis on HPC systems-- #slurm #hpc youtu.be/Sz7LpAC1gsQ
youtu.be
[2025-04-04] Writing nested array jobs at JHPCE and designing run_all.sh scripts
YouTube video by Leonardo Collado Torres
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Reposted by Nick Eagles
🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 18/11/2024
I'm thrilled to share with you that #visiumStitched led by @nick-eagles.bsky.social has now been published Our #RStats / @bioconductor.bsky.social 📦 provides a framework for stitching together multiple #Visium @10xgenomics.bsky.social capture areas together #AcademicSky doi.org/10.1186/s128...
doi.org
Integrating gene expression and imaging data across Visium capture areas with visiumStitched - BMC Genomics
Background Visium is a widely-used spatially-resolved transcriptomics assay available from 10x Genomics. Standard Visium capture areas (6.5mm by 6.5mm) limit the survey of larger tissue structures, bu...
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