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coexpression
•
reset
0
votes
0
replies
824
views
Sample size on Differential Network Analysis
coexpression
WGCNA
3.1 years ago
Hanna
▴ 10
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 7.6 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.5k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 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 4.9 years ago by
Peter Langfelder
★ 3.0k • written 4.9 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 6.0 years ago by
Peter Langfelder
★ 3.0k • written 6.0 years ago by
7kemZmani
▴ 10
0
votes
0
replies
851
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 6.1 years ago by
Peter Langfelder
★ 3.0k • written 6.1 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
6.1 years ago
jol.espinoz
▴ 40
0
votes
0
replies
724
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 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
juls
• 0
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 8.7 years ago by
Peter Langfelder
★ 3.0k • written 8.7 years ago by
abellonau
▴ 60
4
votes
5
replies
6.2k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 8.8 years ago by
Dan Tenenbaum
★ 8.2k • written 8.9 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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