Excited to share with the single-cell community the most recent work of Tomàs Montserrat Ayuso and AnnaEsteveCodina from CNAG, something we think will be a game-changer in #scRNAseq quality control: biorxiv.org/content/10.110… bioRxiv Get ready for the tweetorial! 1/10

Great motivator to head into the weekend: Our donor deconvolution pipeline 'hadge' is out in Genome Biology! genomebiology.biomedcentral.com/articles/10.11… This Nextflow pipeline combines 12 hashing and genotype based deconvolution methods to also enable a novel joint deconvolution strategy

Advancing Cell Segmentation and Morphology Analysis with NVIDIA AI Foundation Model VISTA-2D | interesting work from NVIDIA Technical Blog developer.nvidia.com/blog/advancing…

Using in situ spatial transcriptomics? Try Proseg, @danielcjones’s new cell segmentation method based on probabilistic and Cellular Potts modeling. Great for Vizgen Merscope, 10x Genomics Xenium, and @nanostringtech CosMx data. Preprint & code: (1/n) doi.org/10.1101/2024.0…

1/5 Very happy to share our work on flexible, multiscale cell type assignment for subcellular spatial transcriptomics, now in nature nature.com/articles/s4158…

Saw a few dim reduction posts today about how paCMAP preserves global and local structure better than UMAP. I wanted to show some quick examples of how to run it on your SC data... (1/3)

ICYMI SciPyConf... quak 🦆 is a scalable, interactive data table built with #anywidget - 🖱️ crossfilter & sort millions of rows in real time - 🔄 view any ApacheArrow __dataframe__ - ⚡ powered by Interactive Data Lab mosaic & DuckDB - 📓 materialize sub-views back in Project Jupyter

This "frugal CRISPR kit" costs about $2. It includes a cell-free extract (no living cells), plasmids encoding colorful proteins, and Cas9 + guide RNAs. Students express colorful proteins in the extract & then use CRISPR to cut the protein-coding genes, leading to loss of color.

I'm so excited for the very first scverse conference from September 10-12 in Munich, Germany. We are very close to reaching 100+ participants. We still have spots so please consider joining us: scverse.org/conference2024/

Pertpy: an end-to-end framework for perturbation analysis biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Earlier this week we carried out a preliminary analysis of our first 10x Genomics Xenium prime (5,000 gene) run. We had designed this experiment to get a sense of how the prime chemistry performed compared to the Xenium V1 chemistry.

Let me introduce: InstanSeg 🦠🔬💻👩‍🔬 This *would* have been a short thread about Thibaut Goldsborough’s PhD work… but he solved too many problems. Now it's a long thread about 2 preprints, a whole new approach to cell segmentation & #opensource software to make it easy to use

There's a lot of excitement about foundation models and their ability to learn biology 🧬💻 But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress. biorxiv.org/content/10.110…

While hanging out at image.sc, a resource mostly for microscopy image analysis, sometimes I see people using #ImageJ Fiji napari for "outside science" unusual interesting applications. Here is a small thread of things I saw (1/N)

Conotoxins (cone snail venom) are one of the most deadly neurotoxins found in nature. Here's ConoDL/ConoGen: "an end-to-end conotoxin generation model" biorxiv.org/content/10.110… github.com/xueww/ConoDL

BREAKING NEWS: The 2024 Noble Prize for Medicine has been awarded to Jack the Rat for his contribution to research on phallogigantism and the JAK/STAT signalling pathway. You can read how Jack used AI to conduct his research here: frontiersin.org/journals/cell-…

We’ve just finished writing the missing 15,616 Wikipedia articles to get complete coverage of all 19,255 human genes. We used PaperQA2, which has higher accuracy than existing human-written Wikipedia articles, as judged by blinded biology PhD students and postdocs. 1/5

This is an interesting (and short) paper about biases in forensic evidence. It argues that "an error in statistical reasoning," found in a 2023 paper, is leading to "highly inflated claims" and potentially biasing evidence against a defendant in an ongoing homicide case.