search

phbradley / conga

Clonotype Neighbor Graph Analysis
MIT License
79 stars 18 forks source link

Mouse BCR #58

Open DennisCambridge opened 1 year ago

DennisCambridge commented 1 year ago

Hi Philip!

Thank you so much for this amazing tool! It has helped tremendously with fine T cell annotation in our mice sample. I saw that back in 2020 you added BCR, but only for human. I am wondering if we could do mouse BCR now - thank you so much in advance!

phbradley commented 1 year ago

Hi Dennis, Thanks for the kind words! I'm so glad you have found conga useful. I'm afraid we still haven't added mouse bcrs, in part because I hadn't come across any test data. Do you know of any public datasets we could test things on? Or have a little one we could play with (could share this confidentially pbradley@fredhutch.org)? Take care, Phil

DennisCambridge commented 1 year ago

Hi Phil, Thanks so much for the reply! I found two public datasets: GSE174836 and GSE174739. Would these serve the purpose? Have a great upcoming weekend :D. Cheers, Dennis

sheethal94 commented 1 year ago

Hi Philip,

I'm following up on the conversation because I'm also interested in analyzing mouse BCR data using Conga. Please let me know if you have any updates. Thanks!

dn-ra commented 8 months ago

Hi Philip,

Thanks for your development of Conga. I'm wondering if there is any update on making the tool work for mouse BCR data?

phbradley commented 5 months ago

Hi there-- I'm really sorry for the delay on this. I just added the organism "mouse_ig" to the genes database. Give it a try for mouse BCR data and let me know how it goes.