In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

This vignette demonstrates how to run launch a UCSC Cell Browser instance populated with data from a Seurat object. If you use cell browser, please cite:

UCSC Single Cell Browser

Maximilian Haeussler, Nikolay Markov, Brian Raney, and Lucas Seninge

Documentation: https://cellbrowser.readthedocs.io

knitr::opts_chunk$set(
  tidy = TRUE,
  tidy.opts = list(width.cutoff = 95),
  message = FALSE,
  warning = FALSE,
  fig.height = 20,
  fig.width = 16
)

Prerequisites to install:

• Seurat
• UCSC Cell Browser
• SeuratWrappers
• SeuratData

library(Seurat)
library(SeuratData)
library(SeuratWrappers)

Viewing pbmc3k in a cell browser

InstallData("pbmc3k")
pbmc3k <- LoadData("pbmc3k", type = "pbmc3k.final")
ExportToCellbrowser(pbmc3k, dir = "out", cb.dir = "cb_out", port = 8080, reductions = "umap")

# Remember to stop your cell browser instance when done
StopCellbrowser()

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.