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coexpression
•
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0
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replies
838
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Sample size on Differential Network Analysis
coexpression
WGCNA
3.2 years ago
Hanna
▴ 10
1
vote
1
reply
1.5k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
bioming
▴ 10
5
votes
3
replies
2.1k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 5.0 years ago by
Peter Langfelder
★ 3.0k • written 5.0 years ago by
mikhael.manurung
▴ 270
3
votes
7
replies
2.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 6.1 years ago by
Peter Langfelder
★ 3.0k • written 6.1 years ago by
7kemZmani
▴ 10
0
votes
0
replies
859
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
6.1 years ago
tarun2
• 0
0
votes
1
reply
1.1k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 6.2 years ago by
Peter Langfelder
★ 3.0k • written 6.2 years ago by
hkarakurt
▴ 20
0
votes
0
replies
1.7k
views
How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna
modules
coexpression
networks
6.2 years ago
jol.espinoz
▴ 40
0
votes
0
replies
729
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
6.2 years ago
edoardobertolini
• 0
2
votes
1
reply
1.4k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 6.2 years ago by
Peter Langfelder
★ 3.0k • written 6.2 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.3k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 6.5 years ago by
Lluís Revilla Sancho
▴ 730 • written 6.6 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
1.8k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
juls
• 0
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.4 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.7 years ago by
jol.espinoz
▴ 40
1
vote
0
replies
1.3k
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
8.0 years ago
m.fletcher
▴ 20
3
votes
2
replies
2.5k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 8.1 years ago by
Peter Langfelder
★ 3.0k • written 8.1 years ago by
Alan Smith
▴ 150
2
votes
7
replies
4.6k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 8.2 years ago by
Peter Langfelder
★ 3.0k • written 8.2 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
2.7k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 8.4 years ago by
Peter Langfelder
★ 3.0k • written 8.4 years ago by
michael.ridley6
• 0
13
votes
1
reply
4.6k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 8.8 years ago by
Peter Langfelder
★ 3.0k • written 8.8 years ago by
abellonau
▴ 60
4
votes
5
replies
6.2k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 8.9 years ago by
Dan Tenenbaum
★ 8.2k • written 8.9 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
Recent ...
Replies
Answer: Differential gene expression analysis results
by
ATpoint
★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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