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Frequently Requested Vignettes

Here we provide a series of short vignettes to demonstrate a number of features that are commonly used in Seurat. We’ve focused the vignettes around questions that we frequently receive from users by e-mail. Click on a question to get started, or e-mail us at seuratpackage@gmail.com to request a vignette.

New Features

  1. What are the new features in the latest Seurat release?

Dimensional Reduction

  1. How can I access cell embeddings and gene loadings for PCA?
  2. Can I add a custom dimensional reduction to a Seurat object?

Adding in new data

  1. How do I merge two 10X runs, and keep track of run ID?
  2. How do I add new data into an existing Seurat object?

Seurat object interaction

  1. How do I calculate the number of cells in each cluster, subdivided by replicate?
  2. How do I ‘zoom-in’ on cells from a particular cluster for additional analysis?
  3. How can I compute and compare the average gene expression for different clusters?


  1. How can I adjust contrast and color scales on a FeaturePlot?
  2. Can I manually select cells on a PCA or tSNE plot, and find markers that define them?

Cell Cycle Regression

  1. Can Seurat predict cell cycle phases for each cell based on gene expression?
  2. How can I regress cell cycle effects out of my data?

Differential expression

  1. What differential expression tests are supported in Seurat?
  2. How can I speed up differential expression testing for large datasets?

Multimodal Analysis

  1. How can I add multimodal single-cell data into a Seurat obejct?
  2. For CITE-Seq data, how can I visualize and cluster based on single-cell protein levels?
  3. How can I demultiplex samples, and identify doublets, for data produced with Cell Hashing?

Working with large datasets

  1. Do you have any recommendations for speed and memory efficiency?
  2. How do I analyze datasets that don’t fit into memory?
  3. Where can I find out more about loomR?

Interoperability with other single-cell analysis packages

  1. How can I can covert Seurat objects to/from Bioconductor containers?
  2. Can I take data from a Seurat object and import it into python (and vice versa)?