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In MIGEC, there's a [post-processing step to create a hypermutation graph](https://migec.readthedocs.io/en/latest/post.html), which can be put in cytoscape to be able to visualise the b-cell clonal tr…
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Hi,
I am struggeling with getting MiXCR to output FR4 aa sequences.
I have two IGH sequences, I produce alignments as "mixcr align -s hsa in.fastq out.vdjca", I then export alignments as "mixcr exp…
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We have a list of Stats that we have implemented for v1 of the Stats API for rearrangements.
Do we need all of these for Clones?
What else do we need for Clones?
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Hi,
Why does the first clone targetSequence have different lengths in the same sample with different sequencing data? I want to understand how `AssembleCotigs `work. Is the original sequencing data n…
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> ... test for positive selection anywhere in the genome in **any cohort** of sequenced tumor samples.
Does that even include cohorts which are not any of the 37 PCAWG cancer types?
> **Genic Mo…
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Hi.
I'm wondering when the next version of MiXCR will be released?
I believe it's expected to be AIRR compliant?
I would like to be able to use MiXCR output in the Immcantation pipelines, but …
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The lymphgen colouring example shown in the vignette using ashm_multi_rainbow_plot shows every point in grey. No errors are thrown. The points should be coloured as per the legend, which is actually c…
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We need to create clean versions of the following tables for the upcoming data freeze:
**Quality tables**
- [x] analysis.gene_coverage
- [x] analysis.blocklist
- [x] analysis.coverage
- [x] ana…
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#### What analysis module should be updated and why?
mutational signatures
Based on the literature below, we hypothesize we would see a similar phenomenon in our cohort. That is, samples with …
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/daanhazelaar/katdetectr
Confirm the following by …