Frequently Asked Questions

1. What is the format of the input file?

Answer:SDAS supports output files from SAW count, SAW gef2h5ad, and SAW aggr (alpha ver.); it also supports files prepared by users themselves according to the format description on SDAS Input Data Format Description.

2. The cell annotation module has 5 algorithms: Spotlight, cell2location, RCTD, Tangram. All require corresponding scRNA-Seq data. Does SDAS provide it? If not, how should users prepare it?

Answer:SDAS does not currently provide single-cell data for cell annotation. Users need to prepare h5ad files according to the format description in the user manual.

3. Do the modules in SDAS support scRNA-Seq data analysis? If so, how should users prepare single-cell data?

Answer:The dataProcess, DEG, geneSetEnrichment, inferCNV, CCI, trajectory, and transcription factor analysis modules in SDAS all support scRNA-Seq data analysis. Users can prepare input files (h5ad or rds) according to the user manual.

4. Is there a supported solution for visualizing the results output by each module in SDAS?

Answer:Most modules (except spatialDomain, DEG, geneSetEnrichment) support installing jupyter kernel (ipykernel/IRkernel) in the environment, allowing users to directly use Jupyter Notebook and other interactive environments for plotting.