How to continue TCR-seq downstream analysis by seurat?

Question

[Lianfu]

I have gotten the Output data that I ran cellrange VDJ pipeline, but I don't know how to continue analyzing the outputs. How to continue TCR-seq downstream analysis by seurat? I hope someone can help me, thanks.

Answer 1

[theHumanBorch]

There are a couple of general toolkits for single-cell repertoire analyses.

Python: scirpy or dandelion R: scRepertoire or immunarch

There are a large number of additional software options depending on your exact needs - like multimodal embeddings, TCR clustering etc. Happy to update with others if you can give more details. Disclosure - I am the author of scRepertoire.

Answer 2

[tim]

Hi, I hope you are doing great. I don’t know if you still need aid with your problem but maybe this can help. ImmuneWatch has developed a bioinformatics tool called ImmuneWatch DETECT to annotate the epitope specificity of your T-cell receptor sequences. That way you can differentiate vaccine-specific TCRs from bystander TCRs and see what clonotypes hold relevance. Maybe this could be a solution for you? immunewatch.com/detect-early-access-program/ Disclosure, I am working on the product.