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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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DE paper #95

Open patrickjdanaher opened 3 months ago

patrickjdanaher commented 3 months ago

Blurb / summarize this: https://www.biorxiv.org/content/10.1101/2024.08.02.606405v1.full.pdf

eveilyeverafter commented 3 weeks ago

@dan11mcguire, can you write a short (1-3 paragraph) blog post highlighting this article in the next week or two? You can add the following bib desk entry to the references.bib and reference it like so:

@Vasconcelos2024 shows ...

@article {Vasconcelos2024,
    author = {Vasconcelos, Ana Gabriela and McGuire, Daniel and Simon, Noah and Danaher, Patrick and Shojaie, Ali},
    title = {Differential Expression Analysis for Spatially Correlated Data},
    elocation-id = {2024.08.02.606405},
    year = {2024},
    doi = {10.1101/2024.08.02.606405},
    publisher = {Cold Spring Harbor Laboratory},
    abstract = {Differential expression is a key application of imaging spatial transcriptomics, moving analysis beyond cell type localization to examining cell state responses to microenvironments. However, spatial data poses new challenges to differential expression: segmentation errors cause bias in fold-change estimates, and correlation among neighboring cells leads standard models to inflate statistical significance. We find that ignoring these issues can result in considerable false discoveries that greatly outnumber true findings. We present a suite of solutions to these fundamental challenges, and implement them in the R package smiDE.Competing Interest StatementThe authors have declared no competing interest.},
    URL = {https://www.biorxiv.org/content/early/2024/08/06/2024.08.02.606405},
    eprint = {https://www.biorxiv.org/content/early/2024/08/06/2024.08.02.606405.full.pdf},
    journal = {bioRxiv}
}
dan11mcguire commented 3 weeks ago

123

@patrickjdanaher @eveilyeverafter Scratch space PR in for DE paper and smiDE package