Input File Example

Expression Matrix File Format Description

• st.h5ad: Single-slice or multi-slice spatial transcriptomics expression matrix AnnData object generated by SAW, which must contain raw expression matrix and spatial coordinates information. For details, please refer to SDAS Input Data Format Description.

• st.h5mu: Multi-modal data file output by SAW aggr, can be converted to h5ad via h5mu2h5ad.

• mult.csv: Input file for multi-slice merging.

  • The first line starts with # as the header, including sample name, group information, and absolute path to h5ad, separated by commas. Example content is as follows:

  • In the merged adata file, sample and group information are stored in adata.obs['sampleID'] and adata.obs['group'] respectively.

#sample,group,path
sample1,groupA,sample1.h5ad.path
sample2,groupB,sample2.h5ad.path