Table 1(continued)ToolDescriptionRequirementsTypeInterfaceOperatingsystemPrograminglanguages ReferencesswitchdeAn R package for detectingswitch-like differentialexpression along single-cellRNA-seq trajectories.Switchde assumes genesfollow a sigmoidal pattern ofgene expression and tests fordifferential expression using alikelihood ratio test. It alsoreturns maximum likelihoodestimates (MLE) for thesigmoid parameters, whichallows filtering of genes forup- or downregulation as wellas where along the trajectorythe regulation occursswitchde accepts either anSCESet from Scater [110]oramatrix of gene expressionmeasurements. These shouldideally be in log(TPM + 1)form, but any loggednonnegative expressionmeasurements will workPackageCommandlineUnix/Linux,Mac OS,WindowsR[111]OuijaA statistical framework forlearning pseudotimes fromsingle-cell RNA-seq data.Ouija using only small panelsof marker genes and priorknowledge of gene behaviorUses Bayesian hierarchicalnonlinear factor analysis asimplemented in theprobabilistic programminglanguage StanPackageCommandlineUnix/Linux,Mac OS,WindowsR[112]348 Yungang Xu and Xiaobo Zhou