Differential abundance analysis for bulk TCR-seq data
I am currently analyzing bulk TCR-seq data where we are looking at changes in TCR repertoire based on a treatment. I would like to identify sequences that show statistically significant differential abundance across conditions. As there are no specific tools for doing this type of analysis, I am wondering what would be the best way to go about this.
I came across the following paper, which uses modified version of DESEQ for determining differential abundance.
I have also looked at couple of other papers, which use Fisher's exact test along with multiple testing correction.
As my samples do not have replicates, I am wondering what would be the best way to go about this. I am not a statistician so any advice there would be highly appreciated.
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