We just published a short paper on iMeta to introduce SeqKit's new functionality, performance optimizations, and improved user-friendliness, since the initial publication 7 years ago. onlinelibrary.wiley.com/doi/10.1002/im…

The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.110… w/ Joseph Rich et al. we take a close look. The results are 👀 1/🧵

The authors highlight that UMAP/tSNE preserve neighborhoods and conclude: 'If used properly, 2D (tSNE/UMAP) embeddings will continue to help charting the world of single-cell biology.' Dmitry Kobak Jan Lause 🟦 @janlause.bsky.social🦉
biorxiv.org/content/10.110…

Well-assembled with common methods and annotations actually

Astrobiology!

Miniprot v0.13 released with support of non-standard translation tables, minor improvement to junction accuracy and a couple of bug fixes. github.com/lh3/miniprot/r…

A classical question in all our #Bioinformatics courses: How do I escape vim? 😅😅

I am keyed up to present at the CCDM seminar series this week. I will be showing my results on cannabis flavonoids and more..

Happy to announce that our paper : TreeViewer version 2.2.0 is out with Dr. Giorgio Bianchini! Ecology and Evolution Free Software plotting age distributions, spreadsheet editor, publication quality phylogenies, and more. #Phylogenetics Publication: shorturl.at/nwKN6

Can be worse than that?

If anyone feels the FOMO of not being able to be at the Workshop on Genomics 2024, you can go through the genomics adventure from home! 🤗💻🧬 thanks to the great tutorial put together by Guy Leonard et al! Always one of the favourite sessions of the participants! 🤩 #evomics2024

Ok this is kinda neat:

If you give researchrabbit.ai a scientific paper it will generate a network of references and citations!

They didn’t know

NEW PREPRINT, NEW SOFTWARE

We (Team Thomma @teamthomma.bsky.social) are delighted to announce the release of AMAPEC, an accurate antimicrobial activity predictor for fungal effector proteins.

📰: biorxiv.org/content/10.110…
💻: github.com/fantin-mesny/a…

👇🏼

I've gotten several requests recently for permission to use the notes from my computational biology class:
github.com/pachterlab/BI-…

A reminder that they're licensed under CC BY 4.0: you're free to share and adapt, just give appropriate credit and indicate if changes were made.

🧑‍💻 Happy to announce that sandbox.bio v2 has been released! Same bioinformatics tutorials, but now powered by Linux running in your browser.

Stay tuned, we'll be adding lots more tutorials this year.

🎁 🎄 paper out in Trends in Ecology & Evolution: Divergence time shapes gene reuse during repeated adaptation. Let us know if you have any thoughts/feedback!
sciencedirect.com/science/articl…

BioLLMBench: A Comprehensive Benchmarking of Large Language Models in Bioinformatics biorxiv.org/content/10.110…

The CropGPT project: A call for a global, coordinated effort in precision design breeding driven by AI using biological big-data #comment #MolecularPlant cell.com/molecular-plan…

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