Input File Example

h5ad Data Format Description

• st.h5ad: Spatiotemporal transcriptomics expression matrix AnnData object, which must include the raw expression matrix, gene names, and differential analysis grouping information. For details, please refer to SDAS input data format description. gsea and gsva are based directly on this h5ad file.

• prerank requires that a certain obs column in the st.h5ad file must have geneID and log2FC. The analysis result is similar to gsea, and it is recommended to input the result list of all genes.

• enrichr requires that a certain obs column in the st.h5ad file must have deg_gene_name. It is recommended to input a list of significantly differentially expressed genes.

Database Description (Optional)

• All four enrichment analysis functions support gmt format database files, and all gene names in the database should be uppercase. SDAS comes with standard pre-built human and mouse databases.

• When inputting a custom gmt database, gene information must be uppercase, as the process will convert gene information to uppercase before matching with the database.

• The software has downloaded the human and mouse Msigdb databases by default. If you want to use other databases, you can use other gmt files as needed and specify them with the --gmt parameter in the SDAS software path sdas_deg_enrichment/lib/GSEA_DB.