Eric Johnson comments

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                                            Eric Johnson

Errors with reloading EMBEDR, Simes' method, question about figures

Hello! Sorry for the delay in responding! 1. I will look into finding and posting those figure-generating codes. 2. Can you tell me the initialization you used and the size...

Curse of dimensionality with Nearest Neighbour approaches?

Hello! Thanks for your question! Yes, the curse of dimensionality definitely impacts the accuracy of NN identification, however, the use of "fuzzy" similarities in t-SNE and UMAP helps to circumvent...

Assessing UMAP embedding quality and sweeping across n_neighbours parameter

Hi Oskar! If you want run the code using UMAP, it will ignore the `perplexity` parameter. I will make this clear in the documentation! Thanks for the question!

Assessing UMAP embedding quality and sweeping across n_neighbours parameter

Oh, of course! The perplexity parameter does double duty in that it is involved with how the embedding quality is assessed as well as in running t-SNE. That is, currently,...

How is `cid_full_length` assigned?

Thanks for your help! To make sure I understand: `cid_full_length` is a property of the *contig*, not necessarily of the CDR3. The idea behind indicating this information in the `_report.tsv`...

Question about read aggregation by barcode

For what it's worth, here is my script in case I am doing something dumb with any of the arguments. I find that the algorithm starts to hang in the...

Question about read aggregation by barcode

Amazing! Thank you! It seemed like the sort of next step to take this program, so I'll take a look and see if I can contribute anything as well! Thanks...