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cytodata / awesome-cytodata

A curated list of awesome cytodata resources
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Example Profiling Data #3

Closed gwaybio closed 5 years ago

gwaybio commented 5 years ago

From what I can tell, the three entries (BBBC, IDR, RxRx1) in the datasets resource section include only raw images.

Are there any known examples of resources that provide actual profiles (in addition to raw images)?

One of the major reasons for success in RNA space is that processed matrices are made available alongside raw data. This enables really quick secondary analyses. I haven't really seen much of this for profiling data.

gwaybio commented 5 years ago

It looks like Wawer et al. 2014 provides processed profiles. Maybe it is more common than I thought!

gwaybio commented 5 years ago

some processed profiles here: https://github.com/cytodata/cytodata-hackathon-2018#data-available-on-aws

gwaybio commented 5 years ago

here are some more publicly available profiles:

https://docs.google.com/spreadsheets/d/1iNzLmISGxXmDlmZk_Edw5Pp4WBp3pUsmcp8iR7NUFv4/edit#gid=1262001141

I will add to the list soon!

AnneCarpenter commented 5 years ago

I believe all papers published by our lab provided the processed profiles in some fashion, either as supplementary data or in the github repo for the paper (in carpenterlab umbrella).

gwaybio commented 5 years ago

Great! I feel like I captured them all in #4 except for https://github.com/carpenterlab/2016_bray_natprot. I will add this in the next PR!