text: user4739: Is there a way to import gene list into Seurat to define cell type? The default cell types in Seurat is not enough for our research. For example, we want to mark a subtype of B cells in Seurat, but seems like Seurat only have general B cell, I'm planning to download gene list from Genomic Cytometry, and then import the gene list into Seurat and then Seurat define cell types in the cluster based on the gene list I import. Does Seurat support this function?
  
  user3631: Seurat does not define cell types by name. It clusters and assigns each cell to a cluster, from 0 to X.
  If your data has the cell type (e.g. B,T, Mast cells) it means that someone annotate the clusters so that they have a biological meaning.
  You can assign different names to the clusters by using the AddMetaData function.
  sampleID  cellType
  cell1     B
  cell2     B
  cell3     T
  cell4     T
  
  newMeta <- oldMEta
  newMeta$origType <- newMeta$cellType
  newMeta$cellType <- c("B1","B","Treg","Tkill")
  
  object <- AddMetaData(object, newMeta)
  
  The new metadata should look like 
  sampleID  origType  cellType
  cell1     B         B1
  cell2     B         B
  cell3     T         Treg
  cell4     T         Tkill
  
  You can then swap the labels using SetAllIdent(object = test, id = "cellType"). Your tSNE or uMAp, will now show the new cell types.
  Have a look at Manually define clusters in Seurat and determine marker genes
  
  user4799: You can use scID with your gene list to find the cells that match your gene list. You can then find which cluster in Seurat have these cells. 
  
original_text: 4739: <p>Is there a way to import gene list into Seurat to define cell type? The default cell types in Seurat is not enough for our research. For example, we want to mark a subtype of B cells in Seurat, but seems like Seurat only have general B cell, I'm planning to download gene list from Genomic Cytometry, and then import the gene list into Seurat and then Seurat define cell types in the cluster based on the gene list I import. Does Seurat support this function?</p>
   3631: <p>Seurat does not define cell types by name. It clusters and assigns each cell to a cluster, from 0 to X.
  If your data has the cell type (e.g. B,T, Mast cells) it means that someone annotate the clusters so that they have a biological meaning.</p>
  
  <p>You can assign different names to the clusters by using the <code>AddMetaData</code> function.</p>
  
  <pre><code>sampleID  cellType
  cell1     B
  cell2     B
  cell3     T
  cell4     T
  
  newMeta &lt;- oldMEta
  newMeta<span class="math-container">$origType &lt;- newMeta$</span>cellType
  newMeta$cellType &lt;- c("B1","B","Treg","Tkill")
  
  object &lt;- AddMetaData(object, newMeta)
  </code></pre>
  
  <p>The new metadata should look like </p>
  
  <pre><code>sampleID  origType  cellType
  cell1     B         B1
  cell2     B         B
  cell3     T         Treg
  cell4     T         Tkill
  </code></pre>
  
  <p>You can then swap the labels using <code>SetAllIdent(object = test, id = "cellType")</code>. Your tSNE or uMAp, will now show the new cell types.</p>
  
  <p>Have a look at <a href="https://bioinformatics.stackexchange.com/questions/4249/manually-define-clusters-in-seurat-and-determine-marker-genes?rq=1">Manually define clusters in Seurat and determine marker genes</a></p>
   4799: <p>You can use <a href="https://github.com/BatadaLab/scID" rel="nofollow noreferrer">scID</a> with your gene list to find the cells that match your gene list. You can then find which cluster in Seurat have these cells. </p>
  