Statescope API Reference

Class: `Statescope`

Statescope_model = Initialize_Statescope(Bulk, TumorType='NSCLC')

Parameter	Type	Description
`Bulk`	`pandas.DataFrame`	Bulk gene expression matrix (library-size-corrected counts).
`TumorType`	`str`	Tumor type to select predefined signature (e.g., `"NSCLC"`, `"PDAC"`).
`Ncelltypes`	`int`	Number of cell types in the signature.
`celltype_key`	`str`	Key to use for cell type in AnnData.
`Ncores`	`int`	Number of cores to use for parallel computing.

Function	Description
`Deconvolution()`	Performs Bayesian Log Normal Deconvolution.
`Refinement()`	Refines gene expression after deconvolution.
`StateDiscovery()`	Discovers cellular states using cNMF.

Statescope_model.Deconvolution()

Performs BLADE-based deconvolution on bulk RNA-seq data.

Function	Description
`Initialize_Statescope()`	Initializes the Statescope model with bulk data and signatures.
`fetch_signature()`	Retrieves the precomputed signature matrix.
`list_available_signatures()`	Lists all available signatures.

Statescope_model = Initialize_Statescope(Bulk, TumorType="NSCLC")

Initializes the Statescope object.

Function	Description
`Heatmap_Fractions()`	Plots a heatmap of deconvolution cell type fractions.
`Heatmap_StateScores()`	Visualizes state scores in a heatmap.
`Heatmap_GEX()`	Displays the gene expression matrix.
`TSNE_AllStates()`	Performs t-SNE clustering for all states.
`TSNE_CellTypes()`	Runs t-SNE per cell type.

Heatmap_Fractions(Statescope_model)

Plots a heatmap of cell type proportions per sample.

Function	Description
`Extract_GEX()`	Extracts purified gene expression for a given cell type.
`Extract_StateScores()`	Extracts state scores per sample.
`Extract_StateLoadings()`	Extracts state loadings for gene expression clustering.
`Create_Cluster_Matrix()`	Generates scaled data matrices for clustering.

Extract_GEX(Statescope_model, celltype="T_cells_CD8+")

Retrieves refined gene expression data per cell type.