scrna-orchestrator

You can run a local scRNA-seq analysis workflow by loading raw-count h5ad or 10x Matrix Market inputs into an orchestrator that coordinates QC, normalization, clustering, and marker discovery to generate a reproducible report bundle.

Yes, CellTypist can be used for local cell type annotation within a Scanpy workflow. The orchestrator supports optional CellTypist annotation alongside clustering and marker discovery for comprehensive single-cell analysis.

Two-group contrastive marker analysis can be performed by running an end-to-end scRNA-seq pipeline that supports direct comparison between specified groups, yielding contrastive marker tables alongside standard clustering and QC reports.

Yes, the pipeline supports integrated latent representations, such as X_scvi, as inputs. It processes these latent downstream modes directly, bypassing early preprocessing to generate clustering and marker analysis outputs.

Scrublet is an optional dependency for doublet detection in single-cell RNA-seq analysis. The pipeline enforces reproducibility by producing reports and tables with or without this advanced step, though Scanpy and Anndata are required.

Limitations include the requirement for Scanpy and Anndata environments, while Scrublet and CellTypist remain optional. Inputs must be raw-count h5ad, 10x Matrix Market formats, or integrated latent representations to ensure reproducible analysis bundle generation.