Below is a collection of software tools developed, maintained, or used by our group.
MARQO is an open-source, automated pipeline that streamlines whole-slide, single-cell multiplex imaging analysis by integrating image registration, segmentation, clustering, and user-guided classification to enable high-throughput, spatially resolved quantification and validation of marker co-expression across diverse tissue types and staining methods.
This R script efficiently generates subsampled average expression matrices from Seurat objects by randomly sampling 10% of cells across each cluster and averaging gene expression. It removes empty clusters, builds new Seurat objects per cluster, and merges all into a single object for downstream analyses.