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kspham / coldnet

Combinatorial Disease Network
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Improve the script for download data, multiple type of interaction data, multiple sources. #2

Open kspham opened 9 years ago

damatya commented 9 years ago

I got all PPIs from the Evan Eichler's and Ben's paper (stringDB, HPRD, HINT, Multinet, and iRefIndex). Should I get the BrainSpan Atlas rnaseq data? What about TCGA data (don't think this applies to us)?

kspham commented 9 years ago

Yes, Brain Atlas is good but I think we don't need tcga data. It's for a different disease..

kspham commented 9 years ago

How about Regulatory & RNA networks?

damatya commented 9 years ago

Do you have a database in mind? I'm not familiar with such data. RNA coexpression networks can be constructed from the RNAseq data.

kspham commented 9 years ago

Regulatory network: UniPROBE, JASPAR, TRANSFAC, BCI, Phospho, ELM, NetPhorest, CBS,.... and many newer & better that i don't aware of RNA: 1. We can construct it, 2. TargetScan, PicTar, microRNA, miRBAse, miRDB, TarBase, miRecords,... please explore and decide.

kspham commented 9 years ago

Use functional or object oriented Python. We can't execute every file manually :)

kspham commented 9 years ago

You can use the coding style of one of my previous students as a reference: https://github.com/fenderglass/Ragout