SpaceFold 2.0

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UID: 11343

Author(s): Chu, Tin Yi* * MSK affiliated

Description: Description from GitHub:

"Mapping gene expression cartography from spatial transcriptomics for tissues with stereotypical structures.

What's new?

We developed a new doising method using data diffusion over the imputed SpaceFold axis to oversome sparsity of Visium data and further improve the resolution of cartography over the sliding window mean used by the v1.0 (the SpaceFold paper).

The new version v2.0 is compatible with the new BayesPrism package (https://github.com/Danko-Lab/BayesPrism)."

Subject(s)

Access via GitHub
Access Restrictions: Free to All
Access Instructions: Available under a GPL-2 | GPL-3 license
Associated Publications: Niec R, Chu T, Schernthanner M, Gur-Cohen S, Hidalgo L, Pasolli H, Luckett K, Wang Z, Bhalla S, Cambuli F, Kataru R, Ganesh K, Mehrara B, Pe'er D, Fuchs E. Lymphatics act as a signaling hub to regulate intestinal stem cell activity. Cell Stem Cell. 2022; 29(7):1067-1082.e18.
Software Used: BayesPrism
Bayesian cell Proportion Reconstruction Inferred using Statistical Marginalization (BayesPrism): A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

R
a free software environment for statistical computing and graphics.

roxygen2
Dataset Format(s): R, HTML, MD, Rd

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