| asNNGraph | Function to produce idx and dist representation of a VeloViz graph |
| buildVeloviz | Creates VeloViz graph and FDG layout from PC scores of current and projected transcriptional states. |
| graphViz | Visualize as velocity informed force directed graph |
| normalizeDepth | Normalizes counts to CPM |
| normalizeVariance | Identify overdispersed genes by normalizing counts per million (CPM) gene expression variance relative to transcriptome-wide expectations (Modified from SCDE/PAGODA2 code) |
| pancreas | Pancreas scRNA-seq data |
| plotEmbedding | Plot 2D embedding From scde/pagoda2/MUDAN |
| plotVeloviz | Plot function |
| projectedNeighbors | Computes composite distances between all cell pairs and returns k-nearest neighbors and edge weights needed to build VeloViz graph. |
| reduceDimensions | Reduce dimension using Principal Components Analysis via 'svds' from 'RSpectra' |
| vel | MERFISH velocity subset |
| veloviz | veloviz |