text: user3171:  As it is shown in the picture that we can get the pseudotime plot by using Monocle. I was wondering whether we can use some function like the Seurat FindMarker to find out the differential expression genes between the Double-KO and WT in the  bottom right corner?
  
  user6487:  Seurat FindMarker Doc 
  Yes based upon the R documentation here it seems possible.
  This  Differential expression article  seems to show this is how.
  library(Seurat)
  pbmc <- readRDS(file = "../data/pbmc3k_final.rds")
  # list options for groups to perform differential expression on
  levels(pbmc)
  # Find differentially expressed features between CD14+ and FCGR3A+ Monocytes
  monocyte.de.markers <- FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono")
  # view results
  head(monocyte.de.markers)
  # Find differentially expressed features between CD14+ Monocytes and all other cells, only
  # search for positive markers
  monocyte.de.markers <- FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = NULL, only.pos = TRUE)
  # view results
  head(monocyte.de.markers)
  # Pre-filter features that are detected at <50% frequency in either CD14+ Monocytes or FCGR3A+
  # Monocytes
  head(FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono", min.pct = 0.5))
  #...
  # Test for DE features using the MAST package
  head(FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono", test.use = "MAST"))
  head(FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono", test.use = "DESeq2", max.cells.per.ident = 50))
  
  Maybe something like this would work for you.  Monocle export 
    #replace the monocle_cds with your monocle
    seurat <-exportCDS(monocle_cds, export_to = c("Seurat", "Scater"))
    #This bellow will list the options for ident.1 and ident.2
    levels(seurat) 
    # insert name from levels(seurat) command in parentheses
    head(FindMarkers(seurat, ident.1 = "Double-KO+ Mono", ident.2 = "WT+ Mono", test.use = "DESeq2", max.cells.per.ident = 50))
  
  Hopefully you are able to separate the two groups Double-KO and WT into ident.1 and ident.2 so you can use the function on them. Good luck. As long as the exportCDS function works on your data type you input for cds.
  
original_text: 3171: <p><a href="https://i.stack.imgur.com/kFC32.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/kFC32.jpg" alt="enter image description here"></a> As it is shown in the picture that we can get the pseudotime plot by using Monocle. I was wondering whether we can use some function like the Seurat FindMarker to find out the differential expression genes between the Double-KO and WT in the  bottom right corner?</p>
   6487: <p><a href="https://www.rdocumentation.org/packages/Seurat/versions/3.1.1/topics/FindMarkers" rel="nofollow noreferrer" > Seurat FindMarker Doc </a>
  Yes based upon the R documentation here it seems possible.</p>
  
  <p>This <a href="https://satijalab.org/seurat/v3.1/de_vignette.html" rel="nofollow noreferrer" > Differential expression article </a> seems to show this is how.</p>
  
  <pre><code>library(Seurat)
  pbmc &lt;- readRDS(file = "../data/pbmc3k_final.rds")
  # list options for groups to perform differential expression on
  levels(pbmc)
  # Find differentially expressed features between CD14+ and FCGR3A+ Monocytes
  monocyte.de.markers &lt;- FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono")
  # view results
  head(monocyte.de.markers)
  # Find differentially expressed features between CD14+ Monocytes and all other cells, only
  # search for positive markers
  monocyte.de.markers &lt;- FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = NULL, only.pos = TRUE)
  # view results
  head(monocyte.de.markers)
  # Pre-filter features that are detected at &lt;50% frequency in either CD14+ Monocytes or FCGR3A+
  # Monocytes
  head(FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono", min.pct = 0.5))
  #...
  # Test for DE features using the MAST package
  head(FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono", test.use = "MAST"))
  head(FindMarkers(pbmc, ident.1 = "CD14+ Mono", ident.2 = "FCGR3A+ Mono", test.use = "DESeq2", max.cells.per.ident = 50))
  </code></pre>
  
  <p>Maybe something like this would work for you. <a href="https://rdrr.io/bioc/monocle/man/exportCDS.html" rel="nofollow noreferrer" > Monocle export </a></p>
  
  <pre><code>  #replace the monocle_cds with your monocle
    seurat &lt;-exportCDS(monocle_cds, export_to = c("Seurat", "Scater"))
    #This bellow will list the options for ident.1 and ident.2
    levels(seurat) 
    # insert name from levels(seurat) command in parentheses
    head(FindMarkers(seurat, ident.1 = "Double-KO+ Mono", ident.2 = "WT+ Mono", test.use = "DESeq2", max.cells.per.ident = 50))
  </code></pre>
  
  <p>Hopefully you are able to separate the two groups Double-KO and WT into ident.1 and ident.2 so you can use the function on them. Good luck. As long as the exportCDS function works on your data type you input for cds.</p>
  