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I'm happy to share that out paper on Phantasus, a web-application for visual and interactive gene expression analysis, got out in eLife - the journal elifesciences.org/articles/85722 Here, I'm using it to analyze a random GEO dataset, including basic QC to filter outliers, in under 100 seconds! 1/n

Seems like you can determine sequencing platform from the quality scores alone using a GPT model open.substack.com/pub/aseq/p/usi…

Systematic comparison of sequencing-based spatial transcriptomic methods in Nature Methods In summary: “- Stereo-seq, Slide-tag, Visium shows the better capture efficiency with raw sequencing depth - Slide-seq V2, Visium (probe), DynaSpatial gives the better capture efficiency

$ILMN - Illumina buys Fluent Biosciences to accelerate single-cell analysis seekingalpha.com/news/4123099-i…

Are you missing cells and cell types in your single-cell multiome experiments 10x Genomics? Check out EmptyDropsMultiome MarioniLab

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…

Here we go…repurposing spatial imaging techs to achieve ultra-low to ultra-high, multiplexing, nuclei, cells, single (RNA or Protein), multimodal (RNA and Protein), super cheap! NO SEQUENCING! 10x Genomics @nanostringtech Akoya Biosciences Bruker

🗨️ WANNA TALK TO YOUR CELLS? Try out CellWhisperer – our new multimodal AI that turns single-cell RNA-seq analysis into a conversation. No coding needed, just chat in plain English. Short walkthrough below. Web app & bioRxiv preprint linked in the thread. Let's dive in! (1/9)

This is great! NIAID News have launched a collection of public domain illustrations (currently 550 individual icons) bioart.niaid.nih.gov

The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳 For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread. nature.com/articles/s4159…

scBaseCamp was built by directly mining all publicly accessible 10X Genomics scRNAseq data from the Sequence Read Archive (SRA) With over 230M cells drawn from 21 species, 72 tissues, scBaseCamp is significantly larger and more diverse than existing single-cell data repositories