code from SpaceFold paper

jupyter notebooks and R code and dataset related to the SpaceFold paper. BayesPrism_outs.zip : output from BayesPrism. performed a single run of BayesPrism on each tissue by combining two Visium replicates. sig.rdata: run using signature genes. full.rdata: run using full genes (after a mild selection for expressed genes). SpaceRanger_outs.zip: raw output from the Space Ranger. Note that bam files were excluded to reduce the file size. All other files outputed by Space Ranger were included. features.tsv.gz : gene annotation from Space Ranger. SI_adata_paper.h5ad and LI_adata_paper.h5ad : scanpy-processed single cell data from mouse small and large intestine. The cell state column was used for devonvolution. Note that the raw reads were cell-bender corrected reads, which may differ from the cell ranger ouput from GEO. SI_clustering_paper.ipynb and LI_clustering_paper.ipynb: jupyter notebook for processing the scRNA-seq.