Koshlan Mayer-Blackwell

@sgp79. Thanks for the efforts to improve efficiency of tcrdist3. The [test_bkgd_cntl_nn3_vs_bkgd_cntl_nn2.py](https://github.com/kmayerb/tcrdist3/pull/79/commits/83ef7f3f93cc7d62557a209ff1362f0afb0d1b94) failed. I will try to figure out why, but have limited bandwidth to work on tcrdist3 this week,...

With latest version we've changed the reference DB file: The default is now --- **combo_xcr_2024-03-05.tsv** ```python from tcrdist.repertoire import TCRrep import pandas as pd data = pd.DataFrame({'v_b_gene':['TRBV5-1*01'], 'cdr3_b_aa':['CASSSSSF']}) tr =...

Thanks you for your detailed explanation. Yes please provide a PR and I will try to incorporate it. Best, K On Mon, Oct 17, 2022 at 6:51 AM sgp79 ***@***.***>...

can you provide the code you used to generate this error? On Tue, Oct 11, 2022 at 12:30 AM Tianran1 ***@***.***> wrote: > Hi, I am new to tcrdist. When...

TCRrep has no argument df2. what you want is something like this: """ df = pd.read_csv("dash.csv").head(10) df2 = pd.read_csv("dash.csv") tr = TCRrep(cell_df = df, organism = 'mouse', chains = ['alpha','beta'],...

thanks can you send me the link to the example you were initially using. On Tue, Oct 11, 2022 at 11:56 PM Tianran1 ***@***.***> wrote: > Hi, thanks very much....

will change this: https://tcrdist3.readthedocs.io/en/latest/tcrdistances.html#i-want-distances-from-1-tcr-to-many-tcrs On Wed, Oct 12, 2022 at 2:09 PM tcrdist 3 ***@***.***> wrote: > thanks can you send me the link to the example you were initially...

I think the test works because dash2.csv already has precomputed the other CDR columns, I agree this is a confusing example. Thanks for bringing it to my attention. https://github.com/kmayerb/tcrdist3/blob/master/dash2.csv On...

This is not part of tcrdist3, but the script you are referring is viewable on github (tcrdist2) in case it helps you https://github.com/kmayerb/tcrdist2/blob/API2/tcrdist/preprocess_10X.py This is five years old so may...

Please provide the full code block you were trying to run so I can help you diagnose the problem. Best, K On Thu, Oct 20, 2022 at 2:32 AM QianhuiXu...