Why am I only finding out about this now?! Not quite the split view I would like, but certainly better than only being able to see one script!

Our work from this summer is out as a pre-print! Take a look if you're interested in the cell type assignment of single-cell multiplexed imaging and proteomic data at the million cell scale.

Very excited to share that our paper on cell type assignment is out in Cell Systems. In addition to the updates, we also created an interactive tutorial with some example data showcasing Astir's capabilities for anyone to play around with below: colab.research.google.com/github/camlab-…

Happy to finally share an R package I’ve been working on that provides secure password-protection and in-browser decryption of R Markdown/HTML files. Please try it out and let me know what you think! #rstats Website: mattwarkentin.github.io/fidelius/ GitHub: github.com/mattwarkentin/…

🧑‍🎓🇨🇦 Calling all undergraduate students in Canada! 🌞🤖Summer research opportunity to work with Rod Bremner and myself building ML models to classify YAP-dependent cancer subtypes via U of T Data Sciences Institute (DSI) SUDS program! 🔗Apply: datasciences.utoronto.ca/suds-students/ 📅 Deadline February 7th

I'll be giving a talk on how I create standardized and flexible pipelines to automate common biomedical data processing tasks tomorrow at the Toronto Reproducibility Workshop. Registration is free at: eventbrite.ca/e/2022-toronto…

Wait, hold up, you can add an arrow at the end of an axis line like this? Will Chase blowing my mind!

Happy to share that our new study describing how the inherited non-coding single-nucleotide polymorphism rs55705857 drives IDH-mutant glioma is (finally) published. This was a close collaboration Mayo Clinic Comprehensive Cancer Center science.org/doi/abs/10.112…

Presenting Slide-TCR-seq: our method for measuring the transcriptomes of cells & T cell receptor (TCR) sequences in situ! This collaboration w/ Bryan Iorgulescu, Shuqiang Li, Catherine Wu, and Fei Chen Lab led to some cool findings... cell.com/immunity/fullt… 1/8

I'm helping put on an event with BiotechTO on November 10th. If you're in Toronto and want to join DM me for a promo code to register for free.

Has anyone encountered rmarkdown::render overwriting intermediate files when used in parallel on compute clusters with e.g. Snakemake? Leads to wrong output files/results, but very hard to spot. We have a fix but keen to know if it's common knowledge

Does anybody know a good properly and transparently validated benchmark dataset for HLA typing? The ones we found so far (1000G, GIAB based) seem to be pretty intransparent regarding used allele database, inclusion criteria and validation approaches.

A long magazine article by Todd Lencz and myself covering the current state + pros and cons of embryo screening for adult diseases. We worked hard to make this complex and multidisciplinary subject accessible to all audiences. Enjoy the read! aeon.co/essays/embryo-…

Interested in using scRNA-seq to help design antibody panels for e.g. highly multiplexed imaging experiments? Introducing cytomarker, a web-app for iterative panel design, including metrics and link out to antibody catalogues App ➡️ cytomarker.ai Thread ⬇️ (1/8)

I'm trilled to share that I have been selected as one of the Marathon of Hope Cancer Centres Network Terry Fox Research Institute Health Informatics & Data Science Award recipients. Stay tuned for details on the project 🙂

This macrophage tattoo is made of macrophages! Have you ever wondered why tattoos are permanent? In tattooing, ink is injected into the skin. Some of this ink is expelled with the epidermis o, but the rest remains in the dermis for life. 🧵1/10

How can active and self-supervised learning methods improve the efficiency of human annotation of single-cell data? Our paper exploring this (& more!) is now out ➡️ nature.com/articles/s4146…