Reconstructing Ordered Ontogenic Trajectories
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘roots’ version 1.0
Help Pages
| animPlot | Animation plot |
| animPlotGif | Generates a GIF animating |
| applyGaussianKernelwithVariableSigma | Apply Gaussian Kernel using Laleh Haghverdi's variable sigma |
| bgGeneNorm | Normalise by background gene set |
| calculateVariableSigmas | Calculates sigmas for a distance matrix |
| colGrad | Generates a smooth colour gradient |
| diffuseMat | Generic diffusion function |
| diffuseProj | Predicts diffusion map projection from new data points |
| fastDist | Fast vectorised Euclidean distance calculator |
| filterGenes | Filter genes |
| findLouvain | Louvain clustering on transition matrix |
| fnc | Find next cell function |
| getTraj | Find a plausible developmental journey |
| goggles | View single cell dataset |
| sparseMarkov | Make markov matrix sparse |