When you tell an 'omics lab to dress up for Halloween.. Ryan Corces

I'm very excited to release this project I've been working on for about a year or so now! gia is a high-performance genome interval arithmetic toolkit, written in #rustlang 🦀, with significant performance increases (2x-20x) over #bedtools and #bedops. biorxiv.org/content/10.110…

📣 The special Conda 23.10.0 release is here. #libmamba is now the default solver in the #conda package and environment manager. 💨💨 conda.org/blog/2023-11-0…

Did 10x Genomics just make newer versions of Cell Ranger open source? github.com/10XGenomics/ce… (cc Shaun Jackman, @luizirber). This is a huge win for open, transparent, and reproducible science if it’s the case!

Woww!! 10x Genomics Cell Ranger Code is finally public! License enables only "internal use" of the code but still it's a tremendous leap towards transparency. github.com/10XGenomics/ce…

Sometimes an image is really worth a thousand words Same sample, consecutive sections, VISIUM CytAssist vs Xenium Very nice Sergi Cervilla!

It's happening, the big changes to PyO3 are nearly released. Should give a ~25%+ performance boost to most Rust code for Python. This should be one of the biggest step changes in the Python ecosystem this year. I'm really pleased Pydantic has helped a little.

ATTN: Bioinformatics/Comp Bio people Save this thread for a walkthrough of #Devin AI designing primers for flu detection from scratch! I asked "Help me identify DNA primer candidates for the most recent flu strain in the US" Here's what happened! 🧵 #biotech #compbio

🤯 Homebrew has 35 million users? 🍻 to Mike McQuaid and the whole team!

10x Genomics released new single cell GEM-X assays in March, and we were quick to try it out. FHIL benchmarked 5’ GEM-X against 5’ Next GEM v2 chemistry with sorted T-cells from healthy donor PBMCs and targeted the recommended max for each assay, 20k and 10k respectively.(1/8)

We had a great meeting & and are moving forward with a GitHub org. for planning & developing foundational building blocks for sequence analysis & related tasks in Rust Language. The org. "rust-seq" can be found here github.com/rust-seq. Reach out if you're interested in joining!

Excited to share our Seurat update supporting VisiumHD data from 10x Genomics. We explore and validate the ability of HD to map the spatial localization of individual cell types: satijalab.org/seurat/article…

Technology impacts the reliability of your #singlecell data. An independently conducted study reported that our Chromium Flex and 3' assays outperformed other technologies. See how the others stacked up: biorxiv.org/content/10.110…

We're honored to have been funded by CZI Science in cycle 6 of their EOSS program & look forward to bringing some recent algorithmic advances to widely-used tools & building some new ones as well! Excited to work with Jamshed Khan, Daniel Liu, Noah Cape & others on this!

Globally, millions of individuals are affected by endometrial / uterine disorders, yet the #endometrium and the role of its #cellular #heterogeneity in these disorders have been hugely understudied compared with other human tissues and diseases.

Congratulations to all involved in creating this cellular map of the endometrium, the inner lining of the uterus, during multiple phases of the menstrual cycle.  This work helps advance understanding of the healthy endometrium and conditions such as endometriosis. Nature Genetics

📢 New Feature Alert 🎉 The beta version of Automated Cell Annotation is live in Cloud Analysis! Reduce the burden of manual annotation & visualize cell types instantly to get more accurate #singlecell insights faster. Try it now: bit.ly/3XVOdHe

Congrats to Muzlifah Haniffa & team for the BBC News (UK) feature on how human skin develops from stem cells! 🙌 Using #singlecell & #spatialtranscriptomics, this #HumanCellAtlas study could lead to anti-aging breakthroughs: bit.ly/3UbjK5y (Link to paper in comments)

A comprehensive analysis framework for evaluating commercial single-cell RNA sequencing technologies academic.oup.com/nar/advance-ar… 🧬🖥️🧪 github.com/danledinh/scRN…