Input File Example

h5ad Data Format Description

• test.h5ad: Spatial transcriptome expression matrix AnnData object, which must contain raw expression matrix, cell type annotations and other information. Please refer to SDAS Input Data Format Description for details.

celltype_list Cell Type List File (Optional)

• celltype_list.txt: Custom cell type list file, no header, one cell type per line

Fibroblast
T/NK

TF_list Transcription Factor List File (Optional)

• TF_list.txt: Custom transcription factor list file, no header, one transcription factor per line

CLOCK(+)
E2F3(+)
EBF1(+)
E1S1(+)

Transcription Factor (TF) Database Documentation

• ​Built-in database sources:

  1. ​TF List: Lists all known TF gene symbols for the target species.

     • Source: https://github.com/aertslab/pySCENIC/tree/master/resources

  2. ​Reference Database (Feather file)​: Stores regulatory potential rankings of genes vs. TF binding motifs.

     • Source: https://resources.aertslab.org/cistarget/databases/

  3. ​TF Annotation File: Maps motifs to corresponding TFs.

     • Source: https://resources.aertslab.org/cistarget/motif2tf/

• ​Custom database construction:

  • Refer to:

    • pySCENIC official documentation：https://pyscenic.readthedocs.io/en/latest/

    • CistTarget database guide：https://resources.aertslab.org/cistarget/