Body: <p>I am starting to get interested in protein interactome analysis from single cell/nucleus datasets.</p>
  <p>I found three tools that might be interesting, which are <code>CellPhoneDB</code>, <code>CellChat</code> and <code>ICellNet</code>. However, these tools are limited to human or mouse cells and the developers' tips for using the tool for other species is to find the homologues or orthologues corresponding to the proteins in our species of interest.</p>
  <p>What I understand is that these tools use their own database which has been curated using specific methods, which could mean that you would have to repeat the same steps for your species dataset to get a compatible database format and this could take a lot of time.</p>
  <p>Also, I feel that using homologous proteins to find functional protein networks or protein-protein interactions would lead to many biases such as false positives due to the difference between human and other species proteins.</p>
  <p>So I have a few questions here:</p>
  <ul>
  <li>Has anyone already used this type of tool for species that the tool was not designed for? Did they find the results relevant?</li>
  <li>Are there tools that allow the use of external databases (such as the <code>STRING</code> database)?</li>
  <li>Perhaps you know of a similar tool that has been built specifically for Drosophila melanogaster (which is my species of interest).</li>
  <li>Maybe you know of an alternative way/workaround to this problem ?</li>
  </ul>
  <p>Thanks a lot!</p>
  <p>Edit :</p>
  <ul>
  <li>I found FlyPhoneDB which I am definitly going to test. However, I did not found any workaround for species with no dedicated tools. One reason is probably the time it would take to build such tool, though it would be highly valuable.</li>
  <li>Closing this post because it too broad and generic.</li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-12T21:35:36.520Z
Comments.Text: This question is too broad and generic. Please limit your posts to a specific bioinformatics problem that you have encountered. If you want to ask multiple questions, then post multiple questions. If you want to have a general discussion about a topic, this is not the right place; ask your questions on a discussion forum like [reddit](https://www.reddit.com/r/bioinformatics/).
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-15T15:01:55.363Z
Comments.Text: Sorry, you are right. I thought about posting to reddit but I don't know much about the community, at least not the r/bioinformatics one.
Comments.UserDisplayName: Paul Endymion
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-15T21:15:05.780Z
Comments.Text: Asking the question in the exact way you have here should be fine, with a flair of "discussion"; direct link to the post form [here](https://www.reddit.com/r/bioinformatics/submit?title=Cell%20to%20Cell%20communication%20detection%20tools%20for%20wide%20range%20of%20species)
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-07-16T02:40:26.230Z
Comments.Text: I would recommend simply editing the question to focus on a single topic.You can ask multiple questions.
Comments.UserDisplayName: M__
Tags: <single-cell><networks><protein-protein-interaction>
Title: Cell to Cell communication detection tools for wide range of species
ThreadText: # Cell to Cell communication detection tools for wide range of species
  
  (Asked by: username_0 on 2024-07-11)
  
  I am starting to get interested in protein interactome analysis from single cell/nucleus datasets.
  
  I found three tools that might be interesting, which are `CellPhoneDB`, `CellChat` and `ICellNet`. However, these tools are limited to human or mouse cells and the developers' tips for using the tool for other species is to find the homologues or orthologues corresponding to the proteins in our species of interest.
  
  What I understand is that these tools use their own database which has been curated using specific methods, which could mean that you would have to repeat the same steps for your species dataset to get a compatible database format and this could take a lot of time.
  
  Also, I feel that using homologous proteins to find functional protein networks or protein-protein interactions would lead to many biases such as false positives due to the difference between human and other species proteins.
  
  So I have a few questions here:
  
  * Has anyone already used this type of tool for species that the tool was not designed for? Did they find the results relevant?
  * Are there tools that allow the use of external databases (such as the `STRING` database)?
  * Perhaps you know of a similar tool that has been built specifically for Drosophila melanogaster (which is my species of interest).
  * Maybe you know of an alternative way/workaround to this problem ?
  
  Thanks a lot!
  
  Edit :
  
  * I found FlyPhoneDB which I am definitly going to test. However, I did not found any workaround for species with no dedicated tools. One reason is probably the time it would take to build such tool, though it would be highly valuable.
  * Closing this post because it too broad and generic.
  
  **Tags:** single-cell, networks, protein-protein-interaction
  
  > **Comments:**
  > **username_1**: This question is too broad and generic. Please limit your posts to a specific bioinformatics problem that you have encountered. If you want to ask multiple questions, then post multiple questions. If you want to have a general discussion about a topic, this is not the right place; ask your questions on a discussion forum like [reddit](https://www.reddit.com/r/bioinformatics/).  
  > **username_0**: Sorry, you are right. I thought about posting to reddit but I don't know much about the community, at least not the r/bioinformatics one.  
  > **username_1**: Asking the question in the exact way you have here should be fine, with a flair of "discussion"; direct link to the post form [here](https://www.reddit.com/r/bioinformatics/submit?title=Cell%20to%20Cell%20communication%20detection%20tools%20for%20wide%20range%20of%20species)  
  > **username_2**: I would recommend simply editing the question to focus on a single topic.You can ask multiple questions.  
  
  ---
  
  ## 0 answers
  
  