Differential Expression analysis

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5.8 years ago

shivangi.agarwal800 ▴ 120

Hi

I want to perform DE seq analysis of the transcript data (RNA seq data) obtained from TCGA. Which package should I refer?

RNA-Seq • 1.1k views

ADD COMMENT • link 5.8 years ago by shivangi.agarwal800 ▴ 120

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You have a good paper to read https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8

ADD REPLY • link 5.8 years ago by grant.hovhannisyan ★ 2.6k

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If you are able to use the analyzed data already available in LinkedOmics or cBioPortal you could just go that route.

ADD REPLY • link 5.8 years ago by GenoMax 141k

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Thank you, genomax.

shivangi, I'd recommend reading the LinkedOmics tutorial slideshow (with examples) here.

ADD REPLY • link 5.8 years ago by Ram 43k

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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?

ADD REPLY • link 5.8 years ago by shivangi.agarwal800 ▴ 120

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You should include this information in the original post since this is important. You need raw counts for doing analysis with DESeq2.