Hello everyone! We have created a dataset consisting of different cells with a whole-transcriptome (50M reads). Let's say I have a transcriptome of one expanded cancerous cell, and also I have the transcriptome of the same cells directly removed from the patient cancer. How can I compare the similarities of the two?
Another example: I have cell A transcriptome, and I think that cell A contaminated cell B. Can I compare the cell A transcriptome and cell B transcriptome to infer contamination (or similarity)?
I know there are tools to find immune cell infiltration in tissues based on transcriptome analysis, but how can I compare the similarities between two or more transcriptomics and not a database?
I have found a little about spearman's correlation (which I think would be very weak in whole-transcriptome comparison), but I also found another tool named TROM (https://github.com/Vivianstats/TROM) which does that.
Also I found about funrich, where I can compare my transcriptome to other databases based on more features (proteins etc).
Is there any other method to do this?