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Hi, I am in the process of building a searchable database of antibody and T cell receptor repertoires (here, a "repertoire" is a set of antibody or TCR sequences from a single blood sample from a sing…
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Hi,
I am testing this package with my VDJ data but I found that our output were from Cellranger 5.0, where it miss some columns (see https://github.com/scverse/scirpy/issues/279)
I get errors l…
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Dear Dekosky Lab,
Great paper! I was interested in your technology and downloaded data from PRJNA827461 to have a look myself.
After parsing through my own pipeline, I found that the 'TCR_presort_se…
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### Summary
Our new normalization procedure should recapitulate expected treatment differences with respect to clonality, abundance, and other diversity measure of TCR repertoires. In addition, biolo…
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Hi there,
Congrats on a great work, and thanks for developing this package.
I am attempting to pull TCR-seq data for T cells that also have the GEX/CITE-seq Seurat objects.
**QUESTION 1.** …
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### Summary
We have multiple batches that are run at different times and with different total amounts of DNA placed on the sequencer. We need to be able to normalize the differences in read depth acr…
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Habe gerade das Paper gefunden: [DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires](https://www.nature.com/articles/s41467-021-21879-w)
Zur Vorverarbeit…
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### Description of feature
Apparently this is a thing now (e.g. 10x spatial transcriptomics + mixcr, e.g. in [this paper](https://www.sciencedirect.com/science/article/pii/S1074761322000814?via%3Dihu…
grst updated
2 months ago
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Hi Bram,
I am using RTCR to identify the TCR repertoire from amplicon sequencing. I have some more question abouts the output result.
1) how can get the mapping rate for the fastq reads (MiSeq, …
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Hello,
Thank you for developing so nice software: immunarch.
Thank you in advance for great help!
Best,
Yue
Please see atached files.
[P61_Tumor.csv](https://github.com/immunomind/immu…