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coexpression
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0
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replies
1.2k
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Sample size on Differential Network Analysis
coexpression
WGCNA
4.5 years ago
Hanna
▴ 10
15
votes
17
replies
30k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 4.7 years ago by
Lluís Revilla Sancho
▴ 760 • written 9.0 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
2.3k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 6.0 years ago by
Gordon Smyth
52k • written 6.0 years ago by
bioming
▴ 10
5
votes
3
replies
3.1k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 6.3 years ago by
Peter Langfelder
★ 3.0k • written 6.3 years ago by
mikhael.manurung
▴ 280
3
votes
7
replies
3.2k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 7.4 years ago by
Peter Langfelder
★ 3.0k • written 7.4 years ago by
7kemZmani
▴ 10
0
votes
0
replies
1.1k
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
7.4 years ago
tarun2
• 0
0
votes
1
reply
1.5k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 7.5 years ago by
Peter Langfelder
★ 3.0k • written 7.5 years ago by
hkarakurt
▴ 20
0
votes
0
replies
2.2k
views
How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna
modules
coexpression
networks
7.5 years ago
jol.espinoz
▴ 40
0
votes
0
replies
968
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
7.5 years ago
edoardobertolini
• 0
2
votes
1
reply
2.0k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 7.6 years ago by
Peter Langfelder
★ 3.0k • written 7.6 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.8k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 7.9 years ago by
Lluís Revilla Sancho
▴ 760 • written 7.9 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
2.3k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
juls
• 0
1
vote
0
replies
1.7k
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
9.4 years ago
m.fletcher
▴ 20
3
votes
2
replies
3.0k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 9.4 years ago by
Peter Langfelder
★ 3.0k • written 9.4 years ago by
Alan Smith
▴ 150
2
votes
7
replies
5.5k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 9.5 years ago by
Peter Langfelder
★ 3.0k • written 9.6 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
3.2k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 9.7 years ago by
Peter Langfelder
★ 3.0k • written 9.7 years ago by
michael.ridley6
• 0
13
votes
1
reply
5.8k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 10.1 years ago by
Peter Langfelder
★ 3.0k • written 10.1 years ago by
abellonau
▴ 60
4
votes
5
replies
7.2k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 10.2 years ago by
Dan Tenenbaum
★ 8.2k • written 10.2 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
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Comment: Biological Pathway Database
by
peterparkerrbu
• 0
Having the pathways available in PowerPoint format is a huge plus, as it makes them easy to use for presentations and teaching. The ability…
Comment: WGCNA analysis on RNAseq and proteoimcs data
by
sum31278
• 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning
by
inadequate.peacock.iiag
• 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design
by
Gordon Smyth
52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design
by
James W. MacDonald
68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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