| 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 |