Excited to present at the ASHI Annual Meeting next week on Predicting TCR Specificity in the Age of Single-Cell Sequencing. See you on Monday!

ashiannualmeeting2025.eventscribe.net/agenda.asp?p...

Researching at the intersection of HLA and viral infections - check out the special issue from Viruses.

www.mdpi.com/journal/viru...

scRepertoire now supports exporting clones directly into the immunarch workflow. Removing barriers like it's an anti-PD1.

vignette: www.borch.dev/uploads/scre...

Just resubmited the scRepertoire manuscript. Favorite part of the reviewer suggestions was benchmarking - scRepertoire v2 (yellow) can assign > 1 million TCR clonotypes in 30 seconds! Let's not talk about scRepertoire v1 (green line).

Preprint: www.biorxiv.org/content/10.1...

scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling
www.biorxiv.org/content/10.1...

VDJ space-based trajectory analysis for single-cell immune profiling is coming to R!

Check the dandelionR package (in progress): github.com/tuonglab/dan...
Original Publication: www.nature.com/articles/s41...

Congrats to Qile and the R package: APackOfTheClones to visualize single-cell immune profiling! Fully compatible with scRepertoire too!

The one science tweet that I still think about regularly, posting here for posterity.

New R package immApex for deep learning with immune receptor sequences:

repo: github.com/ncborcherdin...
vignette: www.borch.dev/uploads/scre...

scRepertoire v2 is coming - reach out if you have a feature request and even better, if you want to contribute (and authorship!!). New feature - clonal-based rarefaction analysis. Find out more at: github.com/ncborcherdin...

Preprint for Trex is up, check out a framework for combining sc-GEX and TCR data - www.researchsquare.com/article/rs-3.... Like Ibex, the CNN encoders for TCR sequences are up and integrated into the Seurat/Bioconductor pipeline at github.com/ncborcherdin...

New version of Ibex up later today for single-cell GEX and BCR sequencing. Now at 16 convolutional neural network-based autoencoders trained on over 1.5 million heavy and light chain sequences with more to come: github.com/ncborcherdin...

Coder life hack - loop testing parameters now auto-idents the step it is on and emails me the top 10 iterations when it is done:

First few day on bsky - I am Nick a MD/PhD working on developing computational frameworks to bring TCR sequencing into the clinic at Omniscope. My free time is mostly spent running after my daughter and writing open-source R packages for single-cell sequencing. Excited to meet new people here!