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Nanostring-Biostats / CosMx-Analysis-Scratch-Space

This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
https://nanostring-biostats.github.io/CosMx-Analysis-Scratch-Space/
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will there be future GeoMx blog posts on how to analyze the data? #129

Open acjordan333 opened 4 hours ago

acjordan333 commented 4 hours ago

Hi Bruker/Nanostring team,

Thanks for maintaining the CosMx scratch space blog, which is excellent for those of us who are conducting all our analyses in the command line outside of AtoMx. Are there plans to create something similar for GeoMx (a GeoMx scratch space blog)? The Nov 2021 vignette is great, but I was wondering if there would be updates on topics pertaining to GeoMx such as how to correct for batch effect, best practices for using scoring systems such as GSVA/ssGSEA, detecting spatial patterns in tissues, any updates on getting the best deconvolution results if you don't have matching scRNA data for a study, etc.

Best, Alex

eveilyeverafter commented 3 hours ago

Yes, there are plans to do posts with GeoMx DSP. We'll likely broaden the scope of Scratch Space to include DSP instead of creating a separate blog.

acjordan333 commented 14 minutes ago

Excellent! Thanks for responding so quickly. What's the ETA for additional GeoMx blog posts?