Question

Analysis ready RNA Seq repository

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6.6 years ago

kakaru • 0

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 • 1.9k views

ADD COMMENT • link updated 5.9 years ago by Naim.Mahi ▴ 40 • written 6.6 years ago by kakaru • 0

score 0 · Answer 1 · 2017-09-19

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6.6 years ago

Kevin Blighe 87k

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.

ADD COMMENT • link 6.6 years ago by Kevin Blighe 87k

score 0 · Answer 2 · 2017-09-19

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6.6 years ago

Ron ★ 1.2k

GDC has cancer data processed.

There are 11k samples.

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

ADD COMMENT • link 6.6 years ago by Ron ★ 1.2k

score 0 · Answer 3 · 2017-09-19

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6.6 years ago

igor 13k

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

ADD COMMENT • link 6.6 years ago by igor 13k

score 0 · Answer 4 · 2018-06-12

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5.9 years ago

Naim.Mahi ▴ 40

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

ADD COMMENT • link 5.9 years ago by Naim.Mahi ▴ 40

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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.

ADD REPLY • link 5.9 years ago by igor 13k

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

ADD REPLY • link 5.9 years ago by Naim.Mahi ▴ 40