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I am analyzing data similar to 10X format(seekone DD_5) using TRUST4 , which is single-cell VDJ data with barcodes and UMI. The results of the TRUST4 analysis include both airr and barcode_airr tsv re…
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Hi there, thank you for this amazing tool. My team as been using it a lot (see issue #265) but when I try to reproduce the analysis I came up with a few questions.
I did 10x genomics kit 5` GEX an…
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This came up in a side discussions [here](https://github.com/airr-community/airr-standards/issues/246#issuecomment-587962477) and [here](https://github.com/airr-community/airr-standards/issues/320#iss…
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Hi, I am trying to use the airr output files for the downstream mutation analysis. The analysis tool (Immcantation suite) can take AIRR-format files as input. The tool needs to read two columns from t…
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Hello,
I am trying to analyze bulk RNAseq of preB cells (Hardy fraction D) data from mice and comparing the results of TRUST4 between different conditions. I have three genotypes for my mice, Wild-…
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In the scverse core team the consensus was reached that IO should not be part of the analysis packages (e.g. scanpy, scirpy, muon), but rather in an independent package with minimal dependencies and h…
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Hey guys!
I am running TRUST4 on 10xGenomics RNAseq data. Especially, we make use of the AIRR file for our post-processing analysis.
For a QC protocol, we require the `cell_ids`, however I see tha…
mapo9 updated
6 months ago
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I reviewed the documentation and I have some questions, comments and suggestions on various sections of the document.
## Random comments
Who is the target audience for the document? I am not a …
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Thanks for the nice job!
I have faced with a problem in loading the library example(trust4) as it is provided:
However there is no problem in loading 10x files,
airrTrust = system.file('extd…
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The V1.4 Schema introduces some significant structural schema changes, e.g. single value fields turned into objects. These are significant enough that programs will get runtime errors if the code assu…