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I have problems to parse immunoseq data for the tcR package.
I read issue #74 and #83 and already applied to modification to parse.immunoseq3 as suggested to avoid the error message regarding the cou…
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Hello,
It looks like the latest mixcr release, 3.0.3, is no longer parseable by tcR. The clonotype counts were previously an integer, but are now a float and this is producing an error.
Error i…
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Hi Vadim,
I have a question about a tcR function 'find.clonotype'. I am reading through tcR vignette. One of the examples is to show how to search for a target CDR3 sequence. As shown in the vignet…
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The current function seems to result in errors when there are no singletons but duplicates. It runs the third part of the code (i.e. else) but the value for f1 is NA since this is the value of counts …
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Is it possible to create an additional parameter in this function: .do.norm? Currently it is not possible to specify .do.norm = TRUE when calling the entropy function. (Although you might get the sugg…
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When using the vis.kmer.histogram function, It would be interesting to have the x-axis sorted on decreasing frequency instead of alphabetically. Maybe it is an option to include an additional paramete…
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I'm trying to parse a few hundred immunoSEQ files and I don't think it's ID'ing the columns. Could their be a new format that is not compatible?
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Hi
I'm starting to play with mixcr to test I can run it without problems and I would like few things to know whether you can give me some hints.
I have some RNA samples across four different con…
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The MiAIRR data elements are currently specified in a denormalized way, which introduces a lot of redundancy when thinking about storing it in a file format to be used by analysis tools, as well as pr…
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We're currently training on a set of sequences and then comparing the fit to the training data. It's good that we do in fact fit the training data, but perhaps that's not surprising given the flexibil…