Table 1(continued)Tool
DescriptionRequirementsTypeInterfaceOperatingsystemPrograminglanguages ReferencesLEAPUtilizes the estimatedpseudotime of the cells to findgene co-expression thatinvolves time delay. LEAPsorts cells according to theestimated pseudotime andthen computes the maximumcorrelation of all possible timelags. In addition, LEAP canapply a time series inspiredlag-based correlation analysisto reveal linearly dependentgenetic associationsNAPackageCommandlineUnix/Linux,Mac OS,WindowsR[104]SLICERA method for inferring cellulartrajectories from single-cellRNA-seq data. SLICER useslocally linear embedding toreconstruct cellulartrajectories.NAPackageCommandlineUnix/Linux,Mac OS,WindowsR[105]CellTreeProduces tree structuresoutlining the hierarchicalrelationship between single-cell samples, while identifyinglatent groups of genes that canprovide biological insights.CellTree can infer complexunderlying hierarchicalstructures in cell populationsfrom expression data aloneand also provide biologicalbacking for the model itcreatesA typical use case will require youto run compute.lda on yourexpression data, to fit an LDAmodel, followed by compute.backbone.tree to generate atree structure from the LDAmodelPackageCommandlineUnix/Linux,Mac OS,WindowsR[106]346 Yungang Xu and Xiaobo Zhou