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coexpression
•
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0
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1.0k
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Sample size on Differential Network Analysis
coexpression
WGCNA
3.8 years ago
Hanna
▴ 10
15
votes
17
replies
26k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 4.1 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.3 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.9k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 5.3 years ago by
Gordon Smyth
52k • written 5.3 years ago by
bioming
▴ 10
5
votes
3
replies
2.7k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 5.6 years ago by
Peter Langfelder
★ 3.0k • written 5.6 years ago by
mikhael.manurung
▴ 280
3
votes
7
replies
2.7k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 6.7 years ago by
Peter Langfelder
★ 3.0k • written 6.7 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
6.8 years ago
tarun2
• 0
0
votes
1
reply
1.3k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 6.8 years ago by
Peter Langfelder
★ 3.0k • written 6.8 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
6.8 years ago
jol.espinoz
▴ 40
0
votes
0
replies
848
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
6.9 years ago • updated 6.8 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 6.9 years ago by
Peter Langfelder
★ 3.0k • written 6.9 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 7.2 years ago by
Lluís Revilla Sancho
▴ 760 • written 7.3 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
2.0k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 7.8 years ago by
James W. MacDonald
67k • written 7.8 years ago by
juls
• 0
1
vote
0
replies
1.5k
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
8.7 years ago
m.fletcher
▴ 20
3
votes
2
replies
2.8k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 8.8 years ago by
Peter Langfelder
★ 3.0k • written 8.8 years ago by
Alan Smith
▴ 150
2
votes
7
replies
5.1k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 8.9 years ago by
Peter Langfelder
★ 3.0k • written 8.9 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
3.0k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 9.1 years ago by
Peter Langfelder
★ 3.0k • written 9.1 years ago by
michael.ridley6
• 0
13
votes
1
reply
5.2k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 9.4 years ago by
Peter Langfelder
★ 3.0k • written 9.4 years ago by
abellonau
▴ 60
4
votes
5
replies
6.7k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 9.5 years ago by
Dan Tenenbaum
★ 8.2k • written 9.6 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
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Replies
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Gordon Smyth
52k
Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …
Answer: Mean variance curve troubleshoot filtering
by
Gordon Smyth
52k
You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…
Comment: How do I fix an odd voom plot in a combined dataset?
by
Gordon Smyth
52k
The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…
Comment: How do I fix an odd voom plot in a combined dataset?
by
1sunmic2
• 0
Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
by
Andre
• 0
The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…
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Answer: How do I fix an odd voom plot in a combined dataset?
Answer: How do I fix an odd voom plot in a combined dataset?
Comment: How do I fix an odd voom plot in a combined dataset?
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
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