Covered benchmarking R code at an earlier R Stats session #rstats. We went over how memory works, how SLURM checks its usage, and a few helpful R packages: profvis, bench, and peakRAM-- video here: youtu.be/Ix17HfYB-s8?...

[2026-01-30] Benchmarking code chunks in R

YouTube video by Leonardo Collado Torres

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Earlier this year at R Stats Club @libdrstats.bsky.social #rstats we saw that data-frame manipulation using a DuckDB backend, such as through duckplyr, pretty consistently did better than other performant backends. The video's out on YouTube here! www.youtube.com/watch?v=ikum...

[2026-01-23] A look at performance benchmarks for data manipulation in R

YouTube video by Leonardo Collado Torres

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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)!

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

[2025-07-18] Plots in Python with seaborn and plotnine

YouTube video by Leonardo Collado Torres

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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

[2025-07-11] Tidy manipulation of SingleCellExperiment objects

YouTube video by Leonardo Collado Torres

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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

[2025-06-13] Intro to data.table and dtplyr for data manipulation

YouTube video by Leonardo Collado Torres

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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

[2025-05-23] Introduction to dplyr for data manipulation

YouTube video by Leonardo Collado Torres

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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

[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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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...

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...

doi.org

🇲🇽 Leonardo Collado-Torres@lcolladotor.bsky.social · 2y ago

Is your tissue larger than a #10xGenomics Visium capture area? If you need to stitch together the images but also the gene expression data, check our new preprint describing #visiumStitched We also shared example postmortem human brain data (3 samples) doi.org/10.1101/2024...