Philip Bradley

Hi there, thanks for trying conga, and thanks for the feedback. This error suggests that the list "all_data" is empty, which may be because the preceding loop did not execute....

Hi there, I'm really sorry for the slow reply-- I must have missed the notification when this issue was opened! 1. Yes, the changes are already made in the code...

Hi there, thanks for trying conga! Great question. With 10x VDJ data, it's not uncommon to see pairings between one of the chains (alpha or beta) in a high frequency...

Yes, that email address is correct. Take care, Phil ________________________________ From: chuckzzzz ***@***.***> Sent: Wednesday, November 30, 2022 8:29 AM To: phbradley/conga ***@***.***> Cc: Bradley PhD, Phil ***@***.***>; Comment ***@***.***>...

Hi there, Thanks for the kind words and for letting us know about this issue. I have not seen a new error like this yet, so it might help to...

Great, thanks for that. It looks to me like this could be due to empty values in the `raw_clonotype_id` column of the contigs csv file. I just checked in a...

Hi there @xf78 thanks for your interest in tcr-dist! Can you clarify-- what information from the boxed image would you like? Is it the actual clones that are present in...

Hi there, Thanks for trying conga! The function `conga.plotting.make_tcr_db_match_plot` does just that. It gets called here https://github.com/phbradley/conga/blob/master/scripts/run_conga.py#L800 in the `run_conga.py` script, and it's defined here: https://github.com/phbradley/conga/blob/master/conga/plotting.py#L1811 Let me know if...

Hi there, Sorry for my slow reply (traveling). Take a look at the new answer in the CoNGA README FAQ (at the end), and see if that answers your query....

Hi Aviv, Thanks for trying conga! I've run some really big sets and I haven't run into this yet, very cool! As a quick check, if you manually reduce the...