Table 1.

Main applications of CellTrans and corresponding implemented functions.

ESTIMATION OF	APPLICATION/INTERPRETATION	CORRESPONDING FUNCTION(S)
Transition probabilities	Quantification of cell state transitions Transition hierarchies Detect rare and frequent transitions and conclude responsible mechanisms	celltransitions()
Cell state compositions	Predictions beyond time period of experiments Validate experimental results	celltrans_plot() celltrans_plotPDF()
Equilibrium compositions	Predict equilibrium compositions Validate experimental results	celltransitions()
Time to equilibrium	Plan time periods of experiments Choice of time points of measurement	timeToEquilibrium()