tcrdist3

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Installing with python 3.9.10, Avoid Numpy/Numba/Fisher package conflicts

1

tcrdist3 uses Numba for speed which currently requires numpy < 1.22 (see https://numba.readthedocs.io/en/stable/user/installing.html), but lower version of numpy will not work in Python 3.10, so be sure you don't use...

kmayerb

[Request] Improve Documentation for tabulate

2

Just a tiny issue. I was going through your meta-clonotype discovery and tabulation script, modifying it to work with my mouse data, but I kept having issues with the tabulation...

gcohenJH

About distance threshold

1

I notice that `tcrdist3` is derived from `TCRdist`. I want to know how the distance threshold in `TCRdist` is selected. The [original paper](https://www.nature.com/articles/nature22383) just mentioned that the distance threshold was...

showteeth

import_adaptive_file(f) defaults to human and beta but user won't know that. 1. Add warning 2. And update docs

kmayerb

Setup fails when trying to install parasail-1.2.3 on OSX: Possible solution until requirements are changed ``` pip install parasail==1.2 ```

kmayerb

Beta-users have found that jedi==0.18.0 has caused crashes and prevents autocomplete in IPython Solution until we change requirements officialy: ``` pip uninstall jedi pip install jedi==0.17.2 ```

kmayerb

A to P change in CDR3 but no effect on distance

2

Hi @kmayerb, I came across a case, where two TCRs differ by an A to P change in their CDR3, but their distance is 0. How come? ```python >>> import...

andreas-wilm

Hi there, I was following along with the [CDR3 Motifs](https://tcrdist3.readthedocs.io/en/latest/motif_gallery.html?highlight=from%20tcrdist.rep_diff%20import%20hcluster_diff%20tr.hcluster_df%2C%20tr.Z%20%3D%5C%20%20%20%20%20hcluster_diff(clone_df%20%3D%20tr.clone_df%2C%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20pwmat%20%20%20%20%3D%20tr.pw_beta%20%20%20tr.pw_alpha%2C%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20x_cols%20%3D%20%5B%27epitope%27%5D%2C%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20count_col%20%3D%20%27count%27)) tutorial. I ran into a problem at this block of code. Specifically the hcluster_diff function, which uses the hcluster_tally function,...

JoshYeeXJ

BCR distance

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Hi, I just wonder if I can use this to calculate BCR distance if I replace the reference database file from TR to IG? Or are there any other things...

ChangLu92

`TCRrep._show_incomplete()` does not work

1

When running the TCRrep constructor, if issues are encountered with certain rows, the following message is printed: ``` To see entries with missing values use: tcrdist.repertoire.TCRrep._show_incomplete() ``` ```python tr =...

kamurani