roots1.0 package

Animation plot

Generates a GIF animating

Apply Gaussian Kernel using Laleh Haghverdi's variable sigma

Normalise by background gene set

Calculates sigmas for a distance matrix

Generates a smooth colour gradient

Generic diffusion function

Predicts diffusion map projection from new data points

Fast vectorised Euclidean distance calculator

Filter genes

Louvain clustering on transition matrix

Find next cell function

Find a plausible developmental journey

View single cell dataset

Make markov matrix sparse