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Hi , I generated some weird plots of mutationPositionPlot. I use the script of the website, but the generated plot looks like this:
[S5_mutationPositionPlot_Tree1.pdf](https://github.com/user-attachm…
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Hello,
can vdjer work on whole-exome sequencing data? or how to adjust the parameters to make it work for whole-exome sequencing data?
Thanks much!
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Add a tutorial for BCR (or joint BCR/TCR analysis).
Either as additional tutorial, or replace the TCR tutorial as the main "getting started" tutorial.
The latter may make particularly sense, a…
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Hi, Quentin
Could you add an database for IGoR so it can support mouse IgH analysis? In addition, I have some mouse IgH sequencing data, and could you show me how to build the customized mouse IgH mo…
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Hello, I'm fairly new to python and I've been trying to use the cohorts library to mainly calculate neoantigens in my tumor samples.
I have each tumor's processed BAM and VCF files but I'm having a d…
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How to do somatic hypermutation analysis between two sample sets (3 samples per cohort) Can we do somatic hypermutation analysis from https SMARTer Mouse TCR a/b Profiling Kit? I came across "B cell l…
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In the log file when running this, I often see warnings like:
```
WARNING:py.warnings:/usr/local/pkgs/python2/lib/python2.7/site-packages/scipy/integrate/quadrature.py:170: AccuracyWarning: maxiter (…
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Hi,
command,
mixcr exportClones -vIdentityPercents -vBestIdentityPercent -dIdentityPercents -dBestIdentityPercent -jIdentityPercents -jBestIdentityPercent test.contigs.clns clones.tsv
clones_IG…
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Hello, I have run the TRUST4 based on our bulk RNAseq cohort (PE150bp, ribo-zero), where fastq is input, but the results are not consistent with other immune metrics (GEP based). I want to optimize th…
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Hi Quentin,
How did you obtain the indices of where the anchor index is for the J and V genes in your models? Is there implementation or a feature in IGoR so that it can do this? If not, what was t…