I downloaded GDC TCGA HTSeq Count data from 32 different cancer types and want to process it. My aim is to create density plots of each cancer and compare them. I want to see if the density plots look similar enough so that I can compare the expression levels of a certain gene directly between cancers.
For this, I need to process and normalise the TCGA HTSeq Counts of the tumour samples (not healthy controls). I am relatively new to Bioinformatics and don't know how to approach this. There are packages like DeSeq2 and EdgeR, but they are focussed on differential gene expression. But I am having only one condition (tumour) and am not interested in differential gene expression, but only normalisation to perform gene expression quantification. Could you possibly let me know what steps to perform?
I would be very grateful for any help! Thanks in advance.