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coexpression
•
reset
0
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0
replies
1.1k
views
Sample size on Differential Network Analysis
coexpression
WGCNA
4.0 years ago
Hanna
▴ 10
15
votes
17
replies
27k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 4.2 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.4 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
2.0k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 5.5 years ago by
Gordon Smyth
52k • written 5.5 years ago by
bioming
▴ 10
5
votes
3
replies
2.8k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 5.8 years ago by
Peter Langfelder
★ 3.0k • written 5.8 years ago by
mikhael.manurung
▴ 280
3
votes
7
replies
2.8k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 6.8 years ago by
Peter Langfelder
★ 3.0k • written 6.9 years ago by
7kemZmani
▴ 10
0
votes
0
replies
1.0k
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
6.9 years ago
tarun2
• 0
0
votes
1
reply
1.3k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 7.0 years ago by
Peter Langfelder
★ 3.0k • written 7.0 years ago by
hkarakurt
▴ 20
0
votes
0
replies
2.0k
views
How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna
modules
coexpression
networks
7.0 years ago
jol.espinoz
▴ 40
0
votes
0
replies
870
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
7.0 years ago
edoardobertolini
• 0
2
votes
1
reply
1.7k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 7.0 years ago by
Peter Langfelder
★ 3.0k • written 7.0 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.6k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 7.3 years ago by
Lluís Revilla Sancho
▴ 760 • written 7.4 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
2.1k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 8.0 years ago by
James W. MacDonald
68k • written 8.0 years ago by
juls
• 0
1
vote
0
replies
1.6k
views
Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
gsea
ncrna
coexpression
gene set analysis
gene set testing
8.8 years ago
m.fletcher
▴ 20
3
votes
2
replies
2.9k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 8.9 years ago by
Peter Langfelder
★ 3.0k • written 8.9 years ago by
Alan Smith
▴ 150
2
votes
7
replies
5.2k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 9.0 years ago by
Peter Langfelder
★ 3.0k • written 9.0 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
3.0k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 9.2 years ago by
Peter Langfelder
★ 3.0k • written 9.2 years ago by
michael.ridley6
• 0
13
votes
1
reply
5.3k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 9.6 years ago by
Peter Langfelder
★ 3.0k • written 9.6 years ago by
abellonau
▴ 60
4
votes
5
replies
6.8k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 9.7 years ago by
Dan Tenenbaum
★ 8.2k • written 9.7 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
Recent ...
Replies
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA
by
pammelala304
• 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get()
by
Matthew Thornton
▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data
by
user_bioinfo
• 0
yes actually that's why I did, and its all good! thank you for your response
Comment: batch effect removal for agilent microarray data
by
gaye.yilmaz
• 0
Hello again, Can using inSilicoMerging handle this situation?
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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