In sqjin/nlvelo: RNA velocity estimation using nonlinear models

title: "Interface with other single-cell analysis toolkits" author: "Suoqin Jin" date: "r format(Sys.time(), '%d %B, %Y')" output: html_document mainfont: Arial vignette: > %\VignetteIndexEntry{RNA velocity analysis of cellular dynamics using nlvelo} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

knitr::opts_chunk$set(eval = FALSE)

This vignette shows how to extract the required data for nlvelo from other existing single-cell analysis toolkits, including Seurat.

Extract the following data information for velocity analysis

Cell embedding for visualization
Cell labels
Cell-cell distance matrix

Extract the required data from a Seurat V3 object

The required data can be obtained from the Seurat object by

# Cell embedding for visualization
emb = Embeddings(seurat_object, "umap")
# Cell labels
labels <- Idents(seurat_object) # the cell labels
# Cell-cell distance matrix
cell.dist <- as.dist(1-armaCor(t(Embeddings(seurat_object, "pca"))))

Extract the required data from a Seurat V2 object

The required data can be obtained from the Seurat object by

# Cell embedding for visualization
emb <- seurat_object@dr$umap@cell.embeddings
# Cell labels
labels <- seurat_object@idents # the cell labels
# Cell-cell distance matrix
cell.dist <- as.dist(1-armaCor(t(seurat_object@dr$pca@cell.embeddings)))