Tools: tl

scrnatools.tools.cell_type_similarity	Calculates the cosine similarity of cells to provided cell type signatures.
scrnatools.tools.cluster_de	Calculates DE marker genes for data clusters.
scrnatools.tools.create_cell_type_signature	Creates a pseudobulked cell type gene signature from scRNAseq data.
scrnatools.tools.create_isoform_lookup_tables	Creates the lookup tables for isoform data transcripts and genes.
scrnatools.tools.get_expression_matrix	Extracts the cell x gene expression matrix from an AnnData object.
scrnatools.tools.get_immgen_similarity_signatures	Creates a csv with the immgen cell populations signature data.
scrnatools.tools.isoform_preprocessing	Performs basic preprocessing of kallisto isoform data.
scrnatools.tools.load_isoform_lookup_tables	Loads the lookup tables for an isoform AnnData object.
scrnatools.tools.log_density_ratio	Calculates a differential density ratio of cells grouped by condition and control.
scrnatools.tools.read_kallisto_tcc_matrix	Reads in a kallisto bustools isoform matrix.
scrnatools.tools.save_isoform_lookup_tables	Saves the lookup tables for an isoform AnnData object.