Hello Experts,
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.
https://stm.sciencemag.org/content/6/238/238ra70
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.
Are these patient samples? If yes then you can't do much about replicates. Follow the protocol published for similar samples.
Hi GenoMax Yes.