User: 7kemZmani

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7kemZmani10
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Posts by 7kemZmani

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Comment: C: novice: building gene co-expression network using RNA-Seq data
... okay, I think I'll switch to type = 'signed hybrid' as you suggested in the second article. Thank you! ...
written 12 weeks ago by 7kemZmani10
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Comment: C: novice: building gene co-expression network using RNA-Seq data
... would you mind explaining more why the distance measurement is more appropriate for samples, and not genes? maybe I'm wrong, but aren't they just vectors being compared! ...
written 12 weeks ago by 7kemZmani10
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Comment: C: novice: building gene co-expression network using RNA-Seq data
... would you mind explaining more why the distance measurment is more appropriate for samples, and not genes? maybe I'm wrong, but aren't they just vectors being compared! ...
written 12 weeks ago by 7kemZmani10
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Comment: C: novice: building gene co-expression network using RNA-Seq data
... Thank you Peter for your answer. I also thought that type = "distance" means the Euclidean distance, and I thought it will show somewhere in the help document; yet when you look at the help document: ?WGCNA::adjacency() you see "... for type = "distance", adjacency = (1-(dist/max(dist))^2)^power ...
written 12 weeks ago by 7kemZmani10
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Comment: C: novice: building gene co-expression network using RNA-Seq data
... yes, I learned most of this from their tutorials; however; the last part is not in the tutorial. The reason I didn't continue with the tutorial is because, after showing how to pick soft threshold, they started talking about 'block wise network' and module detection, and things I felt I don't really ...
written 12 weeks ago by 7kemZmani10
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novice: building gene co-expression network using RNA-Seq data
... Hello! Background: I'm new to bioinformatics (CS background) and I was assigned the task of implementing a procedure for metabolic network reconstruction that employs a few context-based methods for gene function annotation, which include mRNA coexpression. Question: I just need to share the detai ...
deseq wgcna rna-seq coexpression method written 3 months ago by 7kemZmani10 • updated 12 weeks ago by Peter Langfelder1.5k
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... find out more about how to use KEGG API here: http://www.kegg.jp/kegg/docs/keggapi.html ...
written 3 months ago by 7kemZmani10
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... 'sco' is the organism code for Streptomyces coelicolor in KEGG ...
written 3 months ago by 7kemZmani10
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Answer: A: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... in Kegg there's no direct gene to compound mapping, however you can have that mapping (indirectly) by running `keggLink` twice one to get gene-EC map, and another one to get EC-compound map, then merge by col to get gene-compound mapping. Here's how to do it: library("KEGGREST") res1 = keggLink ...
written 3 months ago by 7kemZmani10
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Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... in what format/structure you expect the output to be? the API you're looking for is `keggLink`; but KEGG doesn't "link" genes with compounds directly. what you can do is "link" pathways to compounds, and also link genes to pathways. From these two links you can derive the third gene-compounds link ...
written 3 months ago by 7kemZmani10

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