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Hello,
I am trying to decide on whether the new version of MIXCR is compatible for our TCR seq pipeline.
Our TCR Seq pipeline is based on the paper "RNase H-dependent PCR-enabled T Cell Receptor…
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**Question**
In the Chapter `AIR REPERTOIRE`, output is `path_tcr_out = f"{path_data}/TCR_01_preprocessed.h5ad"` in [30. Immune Receptor Profiling](https://www.sc-best-practices.org/air_repert…
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Hello,
I am new in using mixcr but I encounter a problem I can not solve
I have bulk tcrseq data paried end and I am using the following command which do not work
thanks for your help
…
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I've been trying to look for a similar error online but haven't found anything so far... Apologies if I've missed something!
I am trying to use scRepertoire with a Seurat v5 object and have been ha…
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Followed by a discussion with @franasa , @bussec; we have come up with the below schema for cell object.
```
Cell:
discriminator: AIRR
type: object
required:
- cell_id
…
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This is on the VDJServer tenant. I’m getting a permission error for aggregations that use the POST end point (submitLargeAggregation).
```
request for this uri path v1airr/repertoire_1/_aggrs/fac…
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Hi, we are experiencing issues with the **clonalDiversity** function on our scTRCseq/scRNAseq dataset. We have 9 samples, and 3 of them seem to be computing erroneous results, ie the Shannon index is …
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Now that scirpy is part of scverse, we could think of an improved data structure for scAIRR data. See also the discussion at https://github.com/theislab/scanpy/issues/1387.
The challenge with scAI…
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Hi,
I am working with immunarch to analyse my paired RNA data, and I am facing a technical issue.
I used MiXCR to get full TCR/IG sequence using "assembleContigs" parameter. After that, I have l…
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Hi
Likely I have a lot of NAs in my TCR
`quantContig(combined, cloneCall="gene+nt", scale = T)`
![Rplot](https://user-images.githubusercontent.com/43682980/167117304-9496604e-b555-4bcd-98a2-87…