API reference

scdecon is a layered package with a strict, test-enforced dependency direction. The pages below document each public module; the computational core (io, preprocessing, signature, deconvolution) never imports the plotting stack, and the numerical solvers operate on plain NumPy arrays.

Module	Responsibility
scdecon.io	Read/write .h5ad, bulk, and metadata tables (faithful, fixed orientation).
scdecon.preprocessing	QC filtering and normalisation, config-driven.
scdecon.signature	Marker selection and signature-matrix construction.
scdecon.deconvolution	The Solver interface, NNLS/ν-SVR/robust solvers, alignment, deconvolve, and benchmarking.
scdecon.simulation	Pseudobulk simulation with known ground truth.
scdecon.validation	Accuracy metrics (RMSE / Pearson / Spearman).
scdecon.genes	Generic gene-identifier harmonisation.
scdecon.plotting	Figures (signature heatmap, truth-vs-prediction, benchmark).

The command-line interface is documented separately in the CLI reference.