Differential Expression analysis
Hi
I want to perform DE seq analysis of the transcript data (RNA seq data) obtained from TCGA. Which package should I refer?
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shivangi.agarwal800
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You have a good paper to read https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8
If you are able to use the analyzed data already available in LinkedOmics or cBioPortal you could just go that route.
Thank you, genomax.
shivangi, I'd recommend reading the LinkedOmics tutorial slideshow (with examples) here.
Thanks for your comments. I have tpm values of transcripts in normal and cancer patients. Can I perform DE analysis using DESeq or any other R package. If yes, can you share the link for the same?
You should include this information in the original post since this is important. You need raw counts for doing analysis with DESeq2.
Thanks genomax for the information