Adding my own ligand-receptor pair to CellphoneDB

[biotech25]

I'd like to add my own ligand-receptor pair to CellphoneDB.

I checked the CellphoneDB v4 database (https://github.com/ventolab/cellphonedb-data/tree/master/data) files, such as 'complex_input.csv', 'gene_input.csv', 'interaction_input.csv', 'protein_input.csv'. But, it seems that there are no ligand-receptor pair that I want to see in my count input data. Then, which file should I add my own ligand-receptor information to? Should I add my own ligand-receptor information to the all 4 files? Could you give me some explanation?

Thank you, Sanghoon

[ktroule]

Hi,

You will find detailed information regarding the tables in the CellPhoneDB manuscript.

In short, you have to add your interactions to the interaction_input.csv, if you add a protein or complex not present in the database those will also need to be added to either the complex or protein table.

Regards Kevin

[biotech25]

Thank you for your explanation, Kevin! My CellPhoneDB database version was 3. 0 and I could add my own ligand-receptor to interaction_input.csv. It worked. I am going to download version 4.1 and try to add my interactions.

Thank you! Sanghoon

[ktroule]

You should be able to use your previous db with the new CellPhoneDB implementation with minor modifications. Note that we have added a few extra columns to the interaction_input.csv and you need also need a new sources folder in the same directory where the database is.

Check notebooks with prefix T00 to download and create your database here.

[biotech25]

Thank you for your kind explanation. I will follow your instruction, and come back to you if I have more questions. Thank you for your help!