Additional file 9 of Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions

Additional file 9: Table S1. A list of gene markers for macrophages when near tumor cells as opposed to hepatocytes as found by niche-DE. Table S2. A list of gene markers for macrophages when hepatocytes as opposed to tumor cells as found by niche-DE. Table S3. A list of ligand-receptor pairs found by niche-LR for macrophages when near tumor cells. Table S4. A list of (macrophage, tumor)+ genes found by niche-DE in the integrated 10X liver metastasis colorectal cancer data. Table S5. The list of enriched pathways found by enrichR using the gene list in table S4. Table S6. The list of enriched pathways found by enrichR using the gene list in table S1.