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Analysis ready RNA Seq repository

Hi,

Recently recount2 was published:

A: Processed RNA-SEQ Datasets

I wonder if anyone knows about similar resource to recount2? I searched the forum and an Australian resource was mentioned.

Also the EBI expression atlas is good but it seems only provide read counts.

rna-seq repository resource online
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updated by Naim.Mahi • Naim.Mahi • written by kakaru • kakaru

4 answers

For cancer, cBioPortal holds RNA-seq (and other) data on many different types of cancers. You can access them pretty quickly for your chosen cancer type through the Download Data tab.

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written by Kevin Blighe Kevin Blighe

GDC has cancer data processed.

There are 11k samples.

https://portal.gdc.cancer.gov/

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written by Ron Ron

There is also TOIL: https://xenabrowser.net/datapages/?host=https://toil.xenahubs.net

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written by igor igor

Check our newly developed tool GREIN at: https://shiny.ilincs.org/grein/

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written by Naim.Mahi • Naim.Mahi

Looks really nice. Can I suggest adding normalized values in addition to the raw counts? Since you have all the downstream analysis, I assume they are already calculated. That way, users can check the expression pattern of their favorite gene. In my experience, that would be very valuable.

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written by igor igor

Thanks for your suggestion. We are planning to provide the normalized data as well in our upcoming release.

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written by Naim.Mahi • Naim.Mahi

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