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 firstname.lastname@example.org to request a vignette.
- How can I access cell embeddings and gene loadings for PCA?
- Can I add a custom dimensional reduction to a Seurat object?
- How do I merge two 10X runs, and keep track of run ID?
- How do I add new data into an existing Seurat object?
- How do I calculate the number of cells in each cluster, subdivided by replicate?
- How do I ‘zoom-in’ on cells from a particular cluster for additional analysis?
- How can I compute and compare the average gene expression for different clusters?
- How can I adjust contrast and color scales on a FeaturePlot?
- Can I manually select cells on a PCA or tSNE plot, and find markers that define them?
- Can Seurat predict cell cycle phases for each cell based on gene expression?
- How can I regress cell cycle effects out of my data?
- What differential expression tests are supported in Seurat?
- How can I speed up differential expression testing for large datasets?
- How can I add multimodal single cell data into a Seurat obejct?
- For CITE-Seq data, how can I visualize and cluster based on single cell protein levels?
- Do you have any recommendations for speed and memory efficiency?
- How do I analyze datasets that don’t fit into memory?
- Where can I find out more about loomR?