User: 7kemZmani

gravatar for 7kemZmani
7kemZmani10
Reputation:
10
Status:
New User
Location:
Last seen:
1 year, 6 months ago
Joined:
1 year, 7 months ago
Email:
7********@gmail.com

Posts by 7kemZmani

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
602
views
1
answers
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 19 months ago by 7kemZmani10
0
votes
1
answer
602
views
1
answers
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 19 months ago by 7kemZmani10
0
votes
1
answer
602
views
1
answers
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 19 months ago by 7kemZmani10
0
votes
1
answer
602
views
1
answers
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 19 months ago by 7kemZmani10
0
votes
1
answer
602
views
1
answers
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 19 months ago by 7kemZmani10
3
votes
1
answer
602
views
1
answer
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 19 months ago by 7kemZmani10 • updated 19 months ago by Peter Langfelder2.3k
0
votes
2
answers
588
views
2
answers
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 19 months ago by 7kemZmani10
0
votes
2
answers
588
views
2
answers
Comment: C: Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
... 'sco' is the organism code for Streptomyces coelicolor in KEGG ...
written 19 months ago by 7kemZmani10
1
vote
2
answers
588
views
2
answers
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 19 months ago by 7kemZmani10
0
votes
2
answers
588
views
2
answers
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 19 months ago by 7kemZmani10

Latest awards to 7kemZmani

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 251 users visited in the last hour