Nick Eagles

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

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

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)!

[2025-07-18] Plots in Python with seaborn and plotnine YouTube video by Leonardo Collado Torres

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

[2025-07-11] Tidy manipulation of SingleCellExperiment objects YouTube video by Leonardo Collado Torres

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

[2025-06-13] Intro to data.table and dtplyr for data manipulation YouTube video by Leonardo Collado Torres

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

[2025-05-23] Introduction to dplyr for data manipulation YouTube video by Leonardo Collado Torres

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

[2025-04-04] Writing nested array jobs at JHPCE and designing run_all.sh scripts YouTube video by Leonardo Collado Torres

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

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...