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

pp.pca	Principal component analysis [Pedregosa et al., 2011].
tl.tsne	t-SNE [Amir et al., 2013, Pedregosa et al., 2011, van der Maaten and Hinton, 2008].
tl.umap	Embed the neighborhood graph using UMAP [McInnes et al., 2018].
tl.draw_graph	Force-directed graph drawing [Chippada, 2018, Islam et al., 2011, Jacomy et al., 2014].
tl.diffmap	Diffusion Maps [Coifman et al., 2005, Haghverdi et al., 2015, Wolf et al., 2018].

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	Compute 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	Map 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	Filter out genes based on two criteria.
tl.marker_gene_overlap	Calculate an overlap score between data-derived 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].