Answers.Body: <p>Most of your questions are part of the Vignettes on the Seurat home page.<br />
  In the <a href="https://satijalab.org/seurat/v3.2/de_vignette.html" rel="nofollow noreferrer">differential expression</a> Vignette you can see that you can run Student's t-tests in the <code>FindMarkers</code> wrapper function.<br />
  However, simple t-tests may not be the best option for single cell data. There are <a href="https://www.nature.com/articles/nmeth.4612" rel="nofollow noreferrer">many algorithms</a> for DE testing with some being directly accessible through <code>FindMarkers</code>. The alogrithm implemented in <code>MAST</code> is <a href="https://www.embopress.org/doi/10.15252/msb.20188746" rel="nofollow noreferrer">recommended</a> frequently.</p>
  <p>Regarding the box plots you should have a look at the violin plot function of Seurat:</p>
  <pre><code>VlnPlot(SeuratData, c(&quot;gene_of_interest&quot;), group.by = &quot;groups_compared_in_DE_test&quot;)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-29T14:53:12.717Z
Answers.LastActivityDate: 2020-07-29T14:53:12.717Z
Answers.UserDisplayName: PPK
Body: <p>I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between two groups within the Seurat package, even possibly showing these results with box plots? Or any way to extract this information from the Seurat object in order to do this using ggplot or anything of that sort? I don't have any specific examples as I've just been going through the Seurat tutorials trying to understand everything, but if anyone has any sort of advice on the topic I would greatly appreciate it!</p>
  
Tags: <gene><proteins><genome><seurat>
Title: Seurat DE t.test
ThreadText: # Seurat DE t.test
  
  (Asked by: username_0 on 2020-07-22)
  
  I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between two groups within the Seurat package, even possibly showing these results with box plots? Or any way to extract this information from the Seurat object in order to do this using ggplot or anything of that sort? I don't have any specific examples as I've just been going through the Seurat tutorials trying to understand everything, but if anyone has any sort of advice on the topic I would greatly appreciate it!
  
  **Tags:** gene, proteins, genome, seurat
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-07-29. Score: 1
  
  Most of your questions are part of the Vignettes on the Seurat home page.  
  In the [differential expression](https://satijalab.org/seurat/v3.2/de_vignette.html) Vignette you can see that you can run Student's t-tests in the `FindMarkers` wrapper function.  
  However, simple t-tests may not be the best option for single cell data. There are [many algorithms](https://www.nature.com/articles/nmeth.4612) for DE testing with some being directly accessible through `FindMarkers`. The alogrithm implemented in `MAST` is [recommended](https://www.embopress.org/doi/10.15252/msb.20188746) frequently.
  
  Regarding the box plots you should have a look at the violin plot function of Seurat:
  
  ```
  VlnPlot(SeuratData, c("gene_of_interest"), group.by = "groups_compared_in_DE_test")
  
  ```
  
  
  ---
  
  