MagesLab

📢 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🔗➡️

📢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

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: go.nature.com/3IxEk9H Code: github.com/nitzanlab/scPr…

🌮Tacco is now published in Nature Biotechnology: nature.com/articles/s4158… And even more importantly, the package is now also available on conda 🐍: anaconda.org/conda-forge/ta… #SingleCell #spatialomics

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: nature.com/articles/s4146… (open access) #epigenome #evolution #crossspecies #epigenetics [1/9]

🌮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!

🌮If you want to see TACCO in action: we already used TACCO to decipher tumor landscapes: doi.org/10.1101/2022.1…

🌮From molecular to tissue scale (and beyond): TACCO helps you crack your (spatial) omics data! Check out our preprint doi.org/10.1101/2022.1… and Python package github.com/simonwm/tacco Joint work with @moriel_noa @InbalDavidi @KlughammerLab #AvivRegev @mor_nitzan et al. 🧵1/n