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gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
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Reference GRN for ESC to endoderm differentiation #66

Closed mfranke-2 closed 2 years ago

mfranke-2 commented 3 years ago

Hi, I am trying to reproduce Fig 3 from your paper and I was wondering if you could share the GRN for ESC to endoderm differentiation which you determined from the ESCAPE database? Thanks a lot!

agitter commented 3 years ago

We can help with this gold standard file. We haven't included the data from ESCAPE yet because we weren't confident about its redistribution policies. We can look into this to see what we're able to provide.

What format would be useful to you? Are you working in MATLAB or something else?

mfranke-2 commented 3 years ago

Great, thank you! I prefer .txt files but MATLAB files are also fine.

agitter commented 3 years ago

I reviewed the ESCAPE database and did not find any specific license permitting or forbidden redistribution. The main page states "Please cite these papers if you use the resources available from this website."

Xu H, Ang YS, Sevilla A, Lemischka IR, Ma'ayan A. Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells. PLoS Comput Biol. 2014 Aug 14;10(8):e1003777

Xu H, Baroukh C, Dannenfelser R, Chen EY, Tan CM, Kou Y, Kim YE, Lemischka IR, Ma'ayan A. ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database (Oxford). 2013 Jun 21;2013:bat045

@atuldeshpande if we host a processed version of the ESCAPE data in https://github.com/gitter-lab/SINGE-supplemental and specify the same terms, we'll be complying with what the ESCAPE authors request. We could include MATLAB and plain text formats if the files are not too large.

agitter commented 2 years ago

@mfranke-2 thanks for your patience. These files are now available in our supplemental GitHub repository. It took us a while to organize a large batch of new files and scripts that we added to that repository.

You should be able to find everything ESCAPE-related in https://github.com/gitter-lab/SINGE-supplemental/tree/master/escape, including the .txt formatted gold standard data we used in the escape_data subdirectory.

agitter commented 2 years ago

@mfranke-2 I'm closing this issue, but please re-open it if there are other datasets you need.