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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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Add metric QC function #78

Closed lahuuki closed 1 month ago

lahuuki commented 4 months ago

Adding a function to aid/standardize the QC process of new spe objects based off of work in Habenula_Visium, spatial_NAc, and Visium_SPG_AD.

Utilizes scater::isOutlier on three metrics log2(sum_umi), log2(sum_gene), and expr_chrM_ratio*100. Added functionality for handling spots in_tissue=FALSE .