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CORTEX seq-FISH: integration with scRNA-seq data

Banff International Research Station for Mathematical Innovation and Discovery

Mr. Joshua Sodicoff is a Data Sciences BS Student in the lab of Joshua Welsh at the University of Michigan Medical School (https://welch-lab.github.io/people/ ). He addressed the first two questions listed on the github page for the seqfish data. Our primary goal was to integrate seqFISH data with scRNA-seq data to increase resolution and utilize LIGER to account for dataset-specific differences in expression. We also attempted to determine how the number of genes reported in the spatial data impacts the quality of the integrated data and of cell type mappings generated by our method. To address these questions, we analyzed both the provided seqFISH and scRNA-seq datasets, as well as additional scRNA-seq data (from the more recent Tasic visual cortex publication) and STARmap data Code is available at https://github.com/jsodicoff/birs_spatial_integration

Mathematics; Statistics; Biology and other natural sciences

video/mp4

Author affiliation: University of Michigan Medical School

2020-12-14

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/76777

Unreviewed

http://creativecommons.org/licenses/by-nc-nd/4.0/