scSpark: an AI-assisted cloud platform for traceable interpretation of single-cell transcriptomic results

Single-cell RNA sequencing now routinely produces detailed maps of cell types and states, but interpreting a finished project remains harder than it should be. Once the analysis is done, the results are usually handed over as static reports, figure panels and supplementary tables. A biologist who later wants to revisit an annotation, recompute a cell-type proportion or check whether a pathway is specific to one group typically has to return to a bioinformatician rather than explore the data directly. We developed scSpark to close this gap. The platform takes the completed outputs of a single-cell project: cell annotations, embeddings, differential-expression tables, trajectories, cell-cell communication networks and enrichment results—and serves them through a web browser as an interactive workspace. Heavy computation stays upstream: scSpark indexes the precomputed objects under a single project structure and exposes them through six modules for cell annotation, differential analysis, trajectory exploration, cell-cell communication, functional interpretation and AI-assisted result interrogation. Every action in these modules, from a query to a label change, an export or an AI-generated summary, is linked to a specific project version, data object, parameter set and output file, so that any conclusion can be traced back to the evidence behind it. We illustrate the platform by reworking a published periodontitis dataset through this interface. scSpark does not replace upstream pipelines or expert judgement; it is a layer that makes their results easier to inspect, revise and reuse, and that turns a single-cell project from a one-off report into an interpretation others can follow and check.