Michael Love

The first fully Rust version of piscem! scRNA, scATAC, and bulk-RNA -> RAD files, accurately, in low memory, and FAST. And all in Rust :) anaconda.org/channels/bio...

Just found reviewer from @simonpcouch.com: Human-scale LLM code review, as if a member of the tidyverse team were there with you to workshop your code for reproducibility, readability, and resilience. Note it's still very experimental. #Rstats github.com/simonpcouch/...

Given the recent spicy #rstats threads, an important reminder:

There's no single right way to code

If it works for you, that's all that matters really

Be good to your fellow coders

exactly. they aren't the enemy. it's the person still using the wrong editor

Apply to be an Opportunity Scholar at posit::conf(2026) in Houston!
We’re offering 40 full-support scholarships for underrepresented groups in data science. Includes: 🎟️ Conference+Workshop pass 🏨 Hotel stay ✈️ Travel reimbursement
Apply by March 13: posit.co/blog/apply-t...
#positconf2026 #rstats

As I'm updating my NIH Biosketch for the N-th time this year, I made a Jekyll theme for students to familiarize themselves with this CV structure while building their online presence.

Demo: jefworks.github.io/online-biosk...
Fork to modify: github.com/JEFworks/onl...

#JustAcademicThings

We recently updated our paper demonstrating evidence of off-target probe binding affecting the 10x Genomics Xenium spatial transcriptomics platform with key clarifications, new quantifications, and approaches for evaluating custom gene panels: biorxiv.org/content/10.1...

🧵👇1/n

This is so fun :). Now you can build the sshash-rs index from within python as well (and even from a list of Python strings! Like always, it's required that there are no duplicate k-mers; the input must be an SPSS). Query individual k-mers, get their hit info, even create a streaming query engine!

If you are teaching any kind of statistics, probability or modeling classes, you'll love this website. Contains dozens of interactive simulations of random processes, with sliders, different visualizat options, and full numeric log ouput: www.randomservices.org/random/apps/...

`dplyr::if_else()` and `dplyr::case_when()` are up to 30x faster dplyr 1.2.0 comes with much faster and more memory efficient `if_else()` and `case_when()` functions!

Last week we released dplyr 1.2.0, but we left off something VERY important 🙂

`dplyr::if_else()` and `dplyr::case_when()` are now up to 30x faster and use 10x less memory!

We dive into how we achieved these numbers in this new #rstats post!

tidyverse.org/blog/2026/02...

crates.io: Rust Package Registry

@mikelove.bsky.social : There was PyDESeq2, and now there is rust_deseq2! crates.io/crates/rust_...

I started offering career advice to two junior colleagues today in separate meetings, and both times I caught myself thinking that, if I'm honest, I don't have very good advice on navigating the current funding and job climate. I think it's important to say that no one does.

We're donating PyDESeq2 to @scverse.bsky.social for long-term maintenance & development. Python reimplementation of DESeq2, ecosystem member since 2023, now in the hands of one of the best open source communities in omics. Good science requires good open source. github.com/scverse/PyDE...

AlphaGenome is out in @nature.com today along with model weights! 🧬

📄 Paper: www.nature.com/articles/s41...

💻 Weights: github.com/google-deepm...

Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

Our @varianteffect.bsky.social annual reports summarize, celebrate and showcase our collective work.
Read the latest 🔖 zenodo.org/records/1833...
View them all 📖 www.varianteffect.org/annual-repor... #AnnualReport #GlobalAlliance
#FunctionalGenomics #Consortium

🎉 We’re excited to welcome Natalia da Silva and @andrew as new editors for rOpenSci’s Statistical Software Peer Review program!

Their experience in statistics, R, reproducible research, and open science will help strengthen our collaborative, transparent, and community-driven review process […]

in particular

"Whereas DESeq2 assumes normally distributed errors when estimating this trend, here we opt for a Student-t distribution as it leads to inference that is more robust to the presence of outlier genes."

there's a hierarchical model BASiCS from @catavallejos.bsky.social and Nils Eling et al with nice parts

bioconductor.org/packages/rel...

and 2018 paper here

pmc.ncbi.nlm.nih.gov/articles/PMC...

Check out this work from Abdalla Alkhawaja et al in Karen Mohlke's group @klmohlke.bsky.social

Profiling RNA and ATAC of 68k+ nuclei from 39 individuals to better understand mechanism and context for GWAS loci

Excited to share our latest work in @ajhgnews.bsky.social 🧬📄

We mapped the regulatory landscape of human liver at single-nucleus resolution using snMultiome, connecting genetic variants to the cell-type mechanisms underlying cardiometabolic disease.
www.sciencedirect.com/science/arti...

It is a PROBLEM that the new MANDATORY ScienCV platform does not (as far as I can tell) enable one to indicate co-first or co-senior authorship in your bibliography. This is a massive disincentive to collaborative science and it needs to be fixed.

yes very high quality

it's close to material palenight but not the same

great! next, what theme you got going here?

Side by side views of the Positron. The left side has the activity bar on the left in the default position. The right side has the activity bar in the top position.

Screenshot of the Positron IDE showing that the Activity Bar moved from the default position on the left side to the top where it's much smaller. A right-click menu is open next to the “Explorer” label, with the option Activity Bar Position → Top selected. Annotations highlight where to right-click, next to the word Explorer, then choose Activity Bar Position, and then choose Top.

This is the most elite change in #Positron, it's so calming.

#rstats #python #databs

a man wearing a plaid shirt and a purple hat is saying here we go . ALT: a man wearing a plaid shirt and a purple hat is saying here we go .

Our paper on the Expanded Registry of candidate cis-Regulatory Elements (cCREs) is out 🎉
www.nature.com/articles/s41...

To celebrate, here’s a "meme-torial" walkthrough of the science.

Let’s get started 🧵 1/11

We used a similar design in this paper:
www.sciencedirect.com/science/arti...

Found that in cis-MR with multiple colocalising instruments (i.e. multiple indepdent signals colocalise between eQTL and pQTL traits) sign concordance was around 95%:

Clever use of proteomic data to stress-test TWAS and QTL colocalization methods, revealing a high false sign rate. This hypothesis about high-LD and cross-tissue confounding is particularly interesting:

If you like larger sample sizes, then do check out our reprocessed and fine mapped cis-eQTLs and cis-sQTLs (leafCutter and MAJIQ!) from the INTERVAL cohort (whole blood, n up to 4,729)!
zenodo.org/records/1795...

These will be on the eQTL Catalogue FTP soon as well.

cc @yosephbarash.bsky.social

It would be interesting to revisit these specific analyses with eQTL sample sizes in 1000s like in @mikelove.bsky.social 's recent work. IMO it's very plausible that while typical cis-eQTL sample sizes find lots of eQTLs, the relevant ones with enough power for colocalization need a bigger N.