tcrdist3
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kmayerb
flexible CDR based distance metrics
I am trying to use tcrdist3, but it keep giving me this error, I'm unable to use it, help me to sort this issue from tcrdist import preprocess_10X Traceback (most...
TRBV6-2*01 seems to be in the IGMT database but it isn't recognized in the TCRrep? Warning: TRBV6-2*01 gene was not recognized in reference db no cdr seq could be inferred...
Dear @kmayerb Since Pandas version 1.5.0, pandas announced to romove the function **pandas.DataFrame.iteritems** in the future version of pandas, especially pandas v2.2.1 in 2024. See [https://pandas.pydata.org/pandas-docs/version/1.5/reference/api/pandas.DataFrame.iteritems.html](url) I've discovered the issue...
When I run section 6 of the Meta-Clonotypes workflow on my own data, I get an error that says: "ValueError: '*' is not in list." It occurs after running this:...
Is it possible to cluster given only the aminoacids sequences? E.g., a endline separated file containing only the following: ``` SLRDAKETQY AVFTKRTNENI ASTGGTESNQPQH ASSLRDRVQNTLY SVGRGNTEAF CASSLRDRVQNTLYF SVENRLGGETQY SARKQGNEQF ASSFESSAETLY SVGSGLRDTQY...
Hello, In TCRdist3, it seems that I am losing most of my clones (Single-cell paired 10X). I have around 4000 clones, but after running TCRdist3, I only have around ~200....
I'm working on running the sparse implementation as described here: https://tcrdist3.readthedocs.io/en/latest/sparsity.html?highlight=sparse My dataset is very large, with more than 200,000 rows, and whether I run the sparse implementation in a...
Hi kmayerb, Thanks for the nice tool! I've been tuning the ntrim/ctrim parameters and wanted to flag an error - usually, the convention on writing CDR3s should be from N-terminal...
Hello, There seem to be wrong/redundant entries in `alphabeta_gammadelta_db.tsv` that place TRAV under "B" chain, e.g. https://github.com/kmayerb/tcrdist3/blob/master/tcrdist/db/alphabeta_gammadelta_db.tsv#L1053. Is it expected?
Hello, I feel like this should be a "simple" fix. When reading in my TCR a/B chains formatted as tcrdist expects, several easily interpretable errors are thrown in this format:...
