(a) Each rectangle represents a data matrix from an omics technology with cells in columns and features in rows. Data Integration methods can be used to combine these data sets. (b) Each circle represents a cell projected into a two-dimensional space. Cells that are closer have more similar molecular profiles. Different colors indicate different clusters of cells, which have been determined through a clustering algorithm. Clusters are usually identified with cell types. (c) Inferred gene regulatory network. Circles show transcription factors and their target genes. Edges correspond to the interactions between them. (d) Each circle represents a cell in a two-dimensional space. Developmental dynamics, indicated by a black line, are revealed with trajectory inference methods. The cell fate decision boundary separates molecular profiles that develop into different cell types. (e) Each node represents a cell type. The leaves of the tree (lowest nodes) are the observed final cell types, whereas the other cell types are transient. Lines indicate the lineage relationships.