Table 1.

Notation

Symbol	Description
C	The number of conditions in a dataset.
c(i)	The condition label of the ith cell.
Gc	Cumulative distribution function for the pseudotimes of a trajectory under condition c. It represents how cells are distributed along the different lineages.
Hc	Cumulative distribution function for the weights of a trajectory under condition c. It represents how cells are distributed between the different lineages.
J	The number of genes in a scRNA-Seq dataset.
L	The number of lineages in a trajectory.
n	The number of cells in a scRNA-Seq dataset.
sjlc	The smoother that represents the gene expression pattern along lineage l for gene j in condition c. It is a smooth function estimated by tradeSeq.
Ti	The pseudotime for a cell i. For a trajectory with more than one lineage, this is a vector, with one value per lineage. It measures how far the cell has progressed along each lineage.
${\mathcal{T}}_c$	The structure of a trajectory under condition c. It is what trajectory inference methods such as slingshot or monocle3 are trying to identify.
Wi	The weights for a cell i. For a trajectory with more than one lineage, this is a vector, with one value per lineage. It measures how close each cell is to each lineage. A weight of 1 means the cell belongs only to that lineage; a weight of 0 means the cell does not belong to that lineage.
X	A reduced-dimensional representation of the dataset. For example, for UMAP, this is a matrix with two columns, where each row gives the 2D coordinates of a cell in that reduced dimension.
Y	The count matrix. Each cell represents the expression level. of a gene (row-wise) in a cell (column-wise).

The table provides the symbol, as well as a short explanation of what it represents. Symbols are listed in alpha-numerical order.