MagesLab

[Systems Immunology Lab @KlughammerLab]

📢 Out in Nat Med: Single-cell, nucleus & 4 types of spatial expression data across the clinicopathological diversity of metastatic breast cancer!
We find surprising within-patient stability, spatial EMT phenotypes, local immune exclusion, and more + comparison across methods🔗➡️

[Systems Immunology Lab @KlughammerLab]

📢BoReMi for manual registration of spatial expression data 🧬 and microscopy images 🔬. When automated tools fail 🥺 BoReMi is your friend💪. Lightweight Jupyter interface, Single cell matching, Non-linear alignment, and more. #spatial_omics #registration #groundtruth

[Jonathan Karin @JonathanKarin3]

scPrisma is out in @NatureBiotech : scPrisma is a framework for enhancement and filtering of topological signals from #SingleCell data based on spectral template matching. Together with Yoni Bornfeld and @mor_nitzan.
Paper: https://t.co/ys9qtdrPSD
Code: https://t.co/W5awFFbINw

[MagesLab @MagesLab]

🌮Tacco is now published in Nature Biotechnology: https://t.co/axrX4PRsmj And even more importantly, the package is now also available on conda 🐍: https://t.co/cIXKMTKOaJ #SingleCell #spatialomics

[MagesLab @MagesLab]

🌮From molecular to tissue scale (and beyond): TACCO helps you crack your (spatial) omics data!
Check out our preprint https://t.co/B0zzUHLYfc and Python package https://t.co/E0kYqR9Q4U
Joint work with @moriel_noa @InbalDavidi @KlughammerLab #AvivRegev @mor_nitzan et al.
🧵1/n

[Christoph Bock Lab @ CeMM & MedUni Vienna @BockLab]

Our “epigenetic zoo” is finally published! DNA methylation profiles for 580 animal species and 2443 tissue samples provide an evolutionary perspective on the epigenome.
Full paper: https://t.co/0QYIYXJRn6 (open access) #epigenome #evolution #crossspecies #epigenetics [1/9]

[MagesLab @MagesLab]

🌮TACCO would not have been possible without support from Evan Murray, Fei Chen @insitubiology, Orit Rozenblatt-Rosen, and Leslie Gaffney, and the inspiring environments at the @broadinstitute, @GeneCenter_LMU, and @HebrewU!

[MagesLab @MagesLab]

🌮From molecular to tissue scale (and beyond): TACCO helps you crack your (spatial) omics data!
Check out our preprint https://t.co/B0zzUHLYfc and Python package https://t.co/E0kYqR9Q4U
Joint work with @moriel_noa @InbalDavidi @KlughammerLab #AvivRegev @mor_nitzan et al.
🧵1/n

[MagesLab @MagesLab]

🌮If you want to see TACCO in action: we already used TACCO to decipher tumor landscapes: https://t.co/DxpGu6Tm8d