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WGCNA
•
reset
3
votes
4
replies
7.8k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.1 years ago by
Arindam
▴ 80
1
vote
1
reply
138
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
updated 4 weeks ago by
Gordon Smyth
53k • written 4 weeks ago by
A.Barden
▴ 10
0
votes
5
replies
694
views
WGCNA
WGCNA
Normalization
RNASeq
written 6 months ago by
Vishnu
• 0
6
votes
8
replies
5.4k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 5.4 years ago by
Colari19
▴ 60
0
votes
2
replies
5.0k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 8 weeks ago by
quordle
• 0 • written 2.4 years ago by
mauricio.microbiol
• 0
0
votes
1
reply
833
views
WGCNA
WGCNA
DESeq2
updated 5 months ago by
ATpoint
★ 4.9k • written 5 months ago by
bioinformaticssrm2011
• 0
0
votes
2
replies
463
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 8 weeks ago by
conservativepaola
• 0 • written 5 months ago by
Μαρία
• 0
11
votes
6
replies
4.6k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 6 months ago by
Ivo
• 0 • written 9.1 years ago by
2323982403
▴ 60
0
votes
1
reply
688
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 7 months ago by
ATpoint
★ 4.9k • written 7 months ago by
ddrummer0056
• 0
0
votes
1
reply
409
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 7 months ago by
ATpoint
★ 4.9k • written 7 months ago by
Reuben
• 0
0
votes
2
replies
432
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
7 months ago
Vinesh
• 0
0
votes
1
reply
270
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 7 months ago by
ATpoint
★ 4.9k • written 7 months ago by
Harshul
• 0
0
votes
1
reply
553
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 9 months ago by
ATpoint
★ 4.9k • written 9 months ago by
siobhan.dietz
• 0
0
votes
0
replies
373
views
WGCNA module preservation using only adjacency matrix
WGCNA
10 months ago
yang1641
• 0
3
votes
4
replies
1.4k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
11 months ago
sukeshinik5
▴ 20
1
vote
1
reply
800
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 11 months ago by
Lluís Revilla Sancho
▴ 760 • written 11 months ago by
Nasim
• 0
0
votes
0
replies
547
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
11 months ago
Fernanda
• 0
0
votes
1
reply
577
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 12 months ago by
Lluís Revilla Sancho
▴ 760 • written 12 months ago by
emilymily77
• 0
0
votes
1
reply
604
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 12 months ago by
James W. MacDonald
68k • written 12 months ago by
bioinformaticssrm2011
• 0
1
vote
3
replies
4.3k
views
WGNCA kME vs. kIM
WGCNA
updated 15 months ago by
Vitor
• 0 • written 10.0 years ago by
akridgerunner
▴ 30
0
votes
0
replies
466
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
16 months ago
k200987
• 0
0
votes
2
replies
793
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
17 months ago
Gimena
• 0
0
votes
2
replies
878
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
17 months ago
w.cookson
• 0
0
votes
1
reply
640
views
problem with ClusterRepro function
WGCNA
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
1.3k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 19 months ago by
ATpoint
★ 4.9k • written 19 months ago by
Priya
• 0
0
votes
2
replies
1.6k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 21 months ago by
aehall26
• 0
4
votes
3
replies
2.9k
views
WGCNA documentation not available
WGCNA
written 21 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
2.4k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 16 months ago by
mariakenneth147
• 0 • written 2.8 years ago by
pharamac
• 0
0
votes
1
reply
1.5k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 21 months ago by
Vanatta
• 0 • written 3.8 years ago by
mairah.khan
• 0
1
vote
2
replies
1.7k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
21 months ago • updated 20 months ago
Levi
• 0
0
votes
2
replies
730
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
21 months ago
davca
• 0
0
votes
1
reply
977
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 22 months ago by
ATpoint
★ 4.9k • written 22 months ago by
ellen.francis
• 0
1
vote
2
replies
1.2k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 22 months ago by
meenae
▴ 10
0
votes
1
reply
785
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 2.1 years ago by
ATpoint
★ 4.9k • written 2.1 years ago by
jiecn
• 0
0
votes
1
reply
5.0k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 2.1 years ago by
James W. MacDonald
68k • written 2.1 years ago by
chiwut.wong
• 0
1
vote
1
reply
879
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 2.2 years ago by
ATpoint
★ 4.9k • written 2.2 years ago by
khaserdene99
• 0
0
votes
1
reply
1.3k
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 2.2 years ago by
ATpoint
★ 4.9k • written 2.2 years ago by
suphamon.j
▴ 20
2
votes
5
replies
2.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 17 months ago by
Ashley
• 0 • written 2.2 years ago by
zxc741xb
• 0
3
votes
6
replies
1.5k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
966
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
suphamon.j
▴ 20
2
votes
1
reply
1.1k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 2.3 years ago by
andres.firrincieli
▴ 50 • written 2.3 years ago by
hesse.sebastian
▴ 10
0
votes
0
replies
765
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
2.3 years ago
Levi
• 0
3
votes
7
replies
2.3k
views
"Degree values are the same for all nodes in a network imported from WGCNA to Cytoscape using RCy3. Seeking insights and potential causes."
Cytoscape
RCy3
Networkvisualization
WGCNA
2.3 years ago
Ortega-C
▴ 10
0
votes
1
reply
842
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.4 years ago by
ATpoint
★ 4.9k • written 2.4 years ago by
Adam
• 0
0
votes
0
replies
917
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
2.4 years ago
Ortega-C
▴ 10
0
votes
2
replies
1.0k
views
WGCNA problem
WGCNA
updated 2.4 years ago by
Ortega-C
▴ 10 • written 2.4 years ago by
mortezaali
• 0
0
votes
0
replies
914
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.4 years ago
Levi
• 0
0
votes
0
replies
762
views
Module Trait Corelation
WGCNA
2.5 years ago
allanokwaro
• 0
2
votes
3
replies
1.7k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 2.5 years ago by
ATpoint
★ 4.9k • written 2.5 years ago by
suphamon.j
▴ 20
0
votes
0
replies
848
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
2.6 years ago
Sooni
▴ 10
335 results • Page
1 of 7
Recent ...
Replies
Answer: DESeq2 used with zinbwave weights - Differences on contrasts calculations
by
eja.gsee.r.m
• 0
Hi your issue with DESeq2 contrasts and zinbwave weights sounds like it might stem from how weights are integrated during the different con…
Comment: How to analyze Affy data, CEL files not available
by
eja.gsee.r.m
• 0
When analyzing data without raw files like Bobby MAS expression measures t important to work within the limits of the available informatio…
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
by
Gordon Smyth
53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
by
Michael Love
43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq
by
boczniak767
▴ 740
@atpoint Should I first standardise data and then average replicates?
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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