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 [Pedregosa11].
tl.tsne	t-SNE [Maaten08] [Amir13] [Pedregosa11].
tl.umap	Embed the neighborhood graph using UMAP [McInnes18].
tl.draw_graph	Force-directed graph drawing [Islam11] [Jacomy14] [Chippada18].
tl.diffmap	Diffusion Maps [Coifman05] [Haghverdi15] [Wolf18].

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 [Traag18].
tl.louvain	Cluster cells into subgroups [Blondel08] [Levine15] [Traag17].
tl.dendrogram	Computes a hierarchical clustering for the given groupby categories.
tl.dpt	Infer progression of cells through geodesic distance along the graph [Haghverdi16] [Wolf19].
tl.paga	Mapping out the coarse-grained connectivity structures of complex manifolds [Wolf19].

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 [Satija15].
tl.score_genes_cell_cycle	Score cell cycle genes [Satija15].

Simulations

tl.sim

Simulate dynamic gene expression data [Wittmann09] [Wolf18].