Tools

tools.lineage_classifer(data[, modal, ...])	Select cells along lineage branches using pseudotime and fate probabilities.
tools.select_paga_path(data, nodes[, modal, ...])	Select cells along specified nodes in a PAGA graph.
tools.test_association(data[, modal, layer, ...])	Test association between genes and pseudotime, and optionally re-filter significant genes.
tools.build_metacells_SEACells(mdata[, ...])	Build metacells using SEACells for RNA and ATAC modalities in a MuData object.
tools.connect_peaks_genes(data, meta_mdata)	Calculate the correlation between ATAC-seq peaks and gene expression for a list of genes.
tools.MotifScanner([motif_db, ...])	A class for scanning DNA sequences for motifs using position frequency matrices (PFMs).
tools.convert_motif_format(input_path, ...)	Converts between different motif file formats.
tools.get_network_score(gdata[, modal, ...])	Calculate centrality measures for all nodes in a directed graph.
tools.RegDecomp(data[, net_key, ...])	A class for performing tensor decomposition on gene regulatory networks to identify regulatory factors (RegFactors).
tools.extract_regfactor_genes(data[, ...])	Extract TFs or TGs with high loadings for each RegFactor and optionally plot their distributions.
tools.FuncEnrich(gene_sets[, geneset_col, ...])	Performs Over-Representation Analysis (ORA) to identify enriched biological pathways or gene sets from a given list of genes.
tools.infer_signal_pairs(data, meta_mdata, ...)	Infer receptor-to-transcription factor (RTF) downstream activity.