User: shahroze786

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Posts by shahroze786

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Comment: C: Modifying Edge Weights in WGCNA
... Yeah my mistake, couldn't figure out how to fix it. ...
written 14 months ago by shahroze7860
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Comment: A: Modifying Edge Weights in WGCNA
... Yes, this is a follow up question I guess, I learned a little bit since the last. Thanks for your reply on that. So here's the thing, I definitely realize how flexible network construction can be, but there is some confusion. The pipeline `WGCNA` follows is correlation matrix -> adjacency matrix ...
written 14 months ago by shahroze7860
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Modifying Edge Weights in WGCNA
... I am creating a gene expression network and this post is mainly to have someone check my methodology but also I have a question regarding the edge weights that are created using a soft threshold. My plan is to use gene expression data to create a similarity matrix using Pearson's Correlation. Then ...
wgcna network igraph R written 14 months ago by shahroze7860 • updated 14 months ago by Biostar ♦♦ 20
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Comment: C: Weighted Gene Expression Network
... For someone like me the flexibility is sort of the problem, there's always an opportunity to make a change and observe the impact. Quick question, not sure about your particular expertise, but do you know the differences between constructing a gene expression network from Pearson correlation or Eucl ...
written 15 months ago by shahroze7860
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Weighted Gene Expression Network
... I have a basic network question, I've been trying to research the typical methodology behind building a gene expression network. As I understand it so far the steps are as follows: Create pearson correlation matrix -> create adjacency matrix (weighted or unweighted) -> create topological overl ...
wgcna network R written 15 months ago by shahroze7860 • updated 15 months ago by Kevin Blighe44k
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Comment: C: Expression Network vs PPI Network
... Do you know where I could download mouse brain PPI data? I've found sources online but most seem to just provide a web interface to interact with the API... ...
written 16 months ago by shahroze7860
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Expression Network vs PPI Network
... I have a general question regarding the type of information that can be provided by different types of networks. What are the advantages of constructing an expression network for analysis compared to a PPI network? What will one give more in regards to studying a disease for example? If I use basal ...
genome gene network expression protein written 16 months ago by shahroze7860 • updated 16 months ago by fishgolden390
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Gene List and Orthologs
... Currently looking for advice on the best way to collect orthology data for E. Coli. I haven't used OMA before but the goal is to basically acquire a gene list for all E. Coli strains then map those genes to Orthology IDs. I downloaded the AllAll data from OMA for the E. Coli strains but there's a lo ...
orthologs oma e. coli written 16 months ago by shahroze7860 • updated 16 months ago by genomax68k

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