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How can I use R to do many genes survival analysis at the same time?

I plan to use the DESeq2::rlog transformed TCGA HTseq_counts data and the TCGA clinical data to do survival analysis. But I am confused how to do many genes(>10000) survival analysis at the same time.

I would be grateful if you could give insights.

Thank you!!

survival data

RNA_seq data

r tcga survival rna-seq
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updated by Shernan • Shernan • written by 137737756 • 137737756

Try to do it for one gene, then wrap it in a loop?

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written by zx8754 zx8754

To follow on from that, you may consider just looping over the formula for Cox proportional hazards to see which genes are statistically significant from that (and then plotting the curves for those). the Cox proportional hazards model is implemented via coxph in R: A: cox proportional hazard model

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written by Kevin Blighe Kevin Blighe

1 answer

Hi! now you can do this task very easily with my recently developed tool named 'geneSA' (https://github.com/huynguyen250896/geneSA). Give it a try ;)

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written by huynguyen96.dnu • huynguyen96.dnu

Thanks so much for posting this tool! I was able to get it to run on my dataset, but the output table has no results. Have you ever encountered that problem? Thanks in advance!

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written by Shernan • Shernan

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