Tools: tl#

Any transformation of the data matrix that is not preprocessing. In contrast to a preprocessing function, a tool usually adds an easily interpretable annotation to the data matrix, which can then be visualized with a corresponding plotting function.

Embeddings#

Compute densities on embeddings.

tl.embedding_density

Calculate the density of cells in an embedding (per condition).

Clustering and trajectory inference#

tl.leiden

Cluster cells into subgroups [Traag et al., 2019].

tl.louvain

Cluster cells into subgroups [Blondel et al., 2008, Levine et al., 2015, Traag, 2015].

tl.dendrogram

Computes a hierarchical clustering for the given groupby categories.

tl.dpt

Infer progression of cells through geodesic distance along the graph [Haghverdi et al., 2016, Wolf et al., 2019].

tl.paga

Mapping out the coarse-grained connectivity structures of complex manifolds [Wolf et al., 2019].

Data integration#

tl.ingest

Map labels and embeddings from reference data to new data.

Marker genes#

tl.rank_genes_groups

Rank genes for characterizing groups.

tl.filter_rank_genes_groups

Filters out genes based on log fold change and fraction of genes expressing the gene within and outside the groupby categories.

tl.marker_gene_overlap

Calculate an overlap score between data-deriven marker genes and provided markers

Gene scores, Cell cycle#

tl.score_genes

Score a set of genes [Satija et al., 2015].

tl.score_genes_cell_cycle

Score cell cycle genes [Satija et al., 2015].

Simulations#

tl.sim

Simulate dynamic gene expression data [Wittmann et al., 2009] [Wolf et al., 2018].