search

sqjin / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data
GNU General Public License v3.0
637 stars 145 forks source link

Using CellChat in zebrafish #331

Open Letichat opened 2 years ago

Letichat commented 2 years ago

Hi, First thanks for the nice tools.

I would like to use CellChat on zebrafish data. I understood that I have to modify the database and replace human gene name by zebrafish name. I have a table with the match between human gene name and zebrafish gene name. Should I just modify the interaction_input_CellChatDB" file ? Which columns have to be modify? I guess the "ligand" and "receptor" should be modify right? Is the other columns need also to be modify as they contain gene name too.

Thanks

sqjin commented 2 years ago

@Letichat Recently we have built a database for zebrafish and I will update it on github this week. Any gene names in the four files mentioned in the tutorial should be updated.

Letichat commented 2 years ago

Perfect! I will wait for it then. Thanks for your work

jkmorrison commented 2 years ago

Joining this thread for updates on the zebrafish database!

SharonWang commented 2 years ago

@sqjin This is really helpful. Wondering if there are any updates for the zebrafish database yet, are we supposed to update/reinstall the package in order to reflect such update?

sqjin commented 2 years ago

@Letichat @jkmorrison @SharonWang zebrafish database has been updated and please re-install the package. You can access the database via CellChatDB.zebrafish. Please let me know if you find any issues or have new L-R pairs that were not included.

jkmorrison commented 2 years ago

Thank you so much for uploading - this is a really incredible resource. Would it be possible to add vegfa and vegfb interactions with nrp1 to the zebrafish database (vegfaa_nrp1, vegfba_nrp1 have been published - not sure that differences have been identified with these interactions between nrp1a and nrp1b)? If you need any additional info here I'm happy to help/send references.

Letichat commented 2 years ago

Thank you! It is really helpful. I would also support the addition of Vegf/Nrp1 interaction.

SharonWang commented 2 years ago

Dear Suoqin,

Thanks a lot for the update of the database. It is super helpful and appreciated.

We will give it a try and keep you updated on how it goes and if there more interactions that we would like to include.

Best regards,

Xiaonan Wang

发件人: Suoqin @.> 发送时间: 2021年12月13日 20:24 收件人: @.> 抄送: @.>; @.> 主题: Re: [sqjin/CellChat] Using CellChat in zebrafish (Issue #331)

@Letichathttps://github.com/Letichat @jkmorrisonhttps://github.com/jkmorrison @SharonWanghttps://github.com/SharonWang zebrafish database has been updated and please re-install the package. You can access the database via CellChatDB.zebrafish. Please let me know if you find any issues or have new L-R pairs that were not included.

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/sqjin/CellChat/issues/331#issuecomment-992426876, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQXIOHR5LLGLFFAHTJEYMTUQXQXVANCNFSM5I22NVHA. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.