Answers.Body: <p>From <a href="https://github.com/satijalab/seurat/issues/1867#issuecomment-515488209" rel="nofollow noreferrer">Seurat developers:</a></p>
  <blockquote>
  <p>the functions Read10X has an argument gene.column that can be used to change between using the gene name and the ensembl ID when reading in 10x Genomics datasets. You can also use the use.names parameter when using Read10X_h5.&quot;</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-05-31T07:53:08.673Z
Answers.LastActivityDate: 2024-05-31T07:53:08.673Z
Answers.UserDisplayName: Raghad Shuwaikan
Answers.Body: <p>I think BioMart will do the gene ID -&gt; gene name conversion you're after:
  <a href="https://www.ensembl.org/info/data/biomart/index.html" rel="nofollow noreferrer">https://www.ensembl.org/info/data/biomart/index.html</a></p>
  <p>To use BioMart to convert the gene IDs to gene names, you can use the BioMaRt bioconductor R package. Installation and running instructions can be found here: ensembl.org/info/data/biomart/biomart_r_package.html</p>
  <p>For this query, you will need to use the human genes dataset:</p>
  <pre><code>ensembl = useEnsembl(biomart=&quot;ensembl&quot;, dataset=&quot;hsapiens_gene_ensembl&quot;)
  </code></pre>
  <p>Then use your list of gene IDs as the 'Filter', with list of IDs as the values:</p>
  <pre><code>filters = 'ensembl_gene_id' 
  </code></pre>
  <p>Most human protein-coding genes have an associated HGNC symbol, and these are used in Ensembl. Therefore, you can select the 'gene_name' attribute to retrieve the human gene names, and this will usually correspond to the HGNC gene names, as stored in the Ensembl database.</p>
  <p>More information on gene names can be found in the Ensembl documentation: <a href="https://ensembl.org/info/genome/genebuild/gene_names.html" rel="nofollow noreferrer">https://ensembl.org/info/genome/genebuild/gene_names.html</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-11-17T15:58:52.043Z
Answers.LastActivityDate: 2023-11-21T14:11:06.600Z
Answers.LastEditDate: 2023-11-21T14:11:06.600Z
Answers.UserDisplayName: Ben_Moore
Body: <p>I have single cell data which I want to annotate with the seurat package, so I ran this code in R:</p>
  <pre><code>lung.data &lt;- Read10X(data.dir =&quot;C:/Users/Desktop/SINGLE-CELL/DATA&quot;,gene.column = 1)
  
  lung &lt;- CreateSeuratObject(counts = lung.data, project = &quot;lung&quot;, min.cells = 3, min.features = 200)
  </code></pre>
  <p>And the output of the features of this seurat object is:</p>
  <pre><code>    &gt;rownames(lung)
      [1] &quot;ENSG00000000003&quot; &quot;ENSG00000000419&quot;
   [3] &quot;ENSG00000000457&quot; &quot;ENSG00000000460&quot;
   [5] &quot;ENSG00000000938&quot; &quot;ENSG00000000971&quot;
   [7] &quot;ENSG00000001036&quot; &quot;ENSG00000001084&quot;
   [9] &quot;ENSG00000001167&quot; &quot;ENSG00000001460&quot;
  [11] &quot;ENSG00000001461&quot; &quot;ENSG00000001497&quot;
  [13] &quot;ENSG00000001561&quot; &quot;ENSG00000001617&quot;
  [15] &quot;ENSG00000001626&quot; &quot;ENSG00000001629&quot;
  [17] &quot;ENSG00000001630&quot; &quot;ENSG00000001631&quot;
  [19] &quot;ENSG00000002016&quot; &quot;ENSG00000002079&quot;
  </code></pre>
  <p>How can I change the row names of this Seurat Object from Ensembl to gene name, knowing that not all the ensemble genes have conversion to gene name, in order to obtain the seurat object with the gene names as row names and cell names as column names?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-17T17:28:43.077Z
Comments.Text: What is a "gene name"? I checked one of your ENSGs and it looks like a human gene, so does that mean you are only working with human sequences? And, if so, do you then mean the HGNC symbol for the gene? Or do you also need to handle other species?
Comments.UserDisplayName: terdon
Tags: <seurat><single-cell><ensembl>
Title: Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?
ThreadText: # Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?
  
  (Asked by: username_0 on 2023-11-17)
  
  I have single cell data which I want to annotate with the seurat package, so I ran this code in R:
  
  ```
  lung.data <- Read10X(data.dir ="C:/Users/Desktop/SINGLE-CELL/DATA",gene.column = 1)
  
  lung <- CreateSeuratObject(counts = lung.data, project = "lung", min.cells = 3, min.features = 200)
  
  ```
  
  And the output of the features of this seurat object is:
  
  ```
      >rownames(lung)
      [1] "ENSG00000000003" "ENSG00000000419"
   [3] "ENSG00000000457" "ENSG00000000460"
   [5] "ENSG00000000938" "ENSG00000000971"
   [7] "ENSG00000001036" "ENSG00000001084"
   [9] "ENSG00000001167" "ENSG00000001460"
  [11] "ENSG00000001461" "ENSG00000001497"
  [13] "ENSG00000001561" "ENSG00000001617"
  [15] "ENSG00000001626" "ENSG00000001629"
  [17] "ENSG00000001630" "ENSG00000001631"
  [19] "ENSG00000002016" "ENSG00000002079"
  
  ```
  
  How can I change the row names of this Seurat Object from Ensembl to gene name, knowing that not all the ensemble genes have conversion to gene name, in order to obtain the seurat object with the gene names as row names and cell names as column names?
  
  **Tags:** seurat, single-cell, ensembl
  
  > **Comments:**
  > **username_1**: What is a "gene name"? I checked one of your ENSGs and it looks like a human gene, so does that mean you are only working with human sequences? And, if so, do you then mean the HGNC symbol for the gene? Or do you also need to handle other species?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2024-05-31. Score: 2
  
  From [Seurat developers:](https://github.com/satijalab/seurat/issues/1867#issuecomment-515488209)
  
  > the functions Read10X has an argument gene.column that can be used to change between using the gene name and the ensembl ID when reading in 10x Genomics datasets. You can also use the use.names parameter when using Read10X\_h5."
  
  
  ---
  
  ### Answer by username_3 on 2023-11-17. Score: 1
  
  I think BioMart will do the gene ID -> gene name conversion you're after:
  <https://www.ensembl.org/info/data/biomart/index.html>
  
  To use BioMart to convert the gene IDs to gene names, you can use the BioMaRt bioconductor R package. Installation and running instructions can be found here: ensembl.org/info/data/biomart/biomart\_r\_package.html
  
  For this query, you will need to use the human genes dataset:
  
  ```
  ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl")
  
  ```
  
  Then use your list of gene IDs as the 'Filter', with list of IDs as the values:
  
  ```
  filters = 'ensembl_gene_id' 
  
  ```
  
  Most human protein-coding genes have an associated HGNC symbol, and these are used in Ensembl. Therefore, you can select the 'gene\_name' attribute to retrieve the human gene names, and this will usually correspond to the HGNC gene names, as stored in the Ensembl database.
  
  More information on gene names can be found in the Ensembl documentation: <https://ensembl.org/info/genome/genebuild/gene_names.html>
  
  
  ---
  
  