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WGCNA
•
reset
6
votes
6
replies
3.8k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.6 years ago by
Colari19
▴ 60
0
votes
0
replies
86
views
WGCNA module preservation using only adjacency matrix
WGCNA
7 days ago
yang1641
• 0
3
votes
4
replies
423
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
5 weeks ago
sukeshinik5
▴ 20
1
vote
1
reply
277
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 6 weeks ago by
Lluís Revilla Sancho
▴ 760 • written 6 weeks ago by
Nasim
• 0
0
votes
0
replies
179
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
8 weeks ago
Fernanda
• 0
0
votes
1
reply
255
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 9 weeks ago by
Lluís Revilla Sancho
▴ 760 • written 9 weeks ago by
emilymily77
• 0
0
votes
1
reply
273
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 10 weeks ago by
James W. MacDonald
67k • written 10 weeks ago by
bioinformaticssrm2011
• 0
0
votes
6
replies
2.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 19 months ago by
mauricio.microbiol
• 0
1
vote
3
replies
3.4k
views
WGNCA kME vs. kIM
WGCNA
updated 6 months ago by
Vitor
• 0 • written 9.2 years ago by
akridgerunner
▴ 30
0
votes
0
replies
242
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
6 months ago
k200987
• 0
0
votes
2
replies
468
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
7 months ago
Gimena
• 0
0
votes
2
replies
535
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
7 months ago
w.cookson
• 0
0
votes
1
reply
383
views
problem with ClusterRepro function
WGCNA
updated 8 months ago by
James W. MacDonald
67k • written 8 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
746
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 9 months ago by
ATpoint
★ 4.5k • written 9 months ago by
Priya
• 0
0
votes
2
replies
1.0k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 11 months ago by
aehall26
• 0
4
votes
3
replies
1.9k
views
WGCNA documentation not available
WGCNA
written 11 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
1.5k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 6 months ago by
mariakenneth147
• 0 • written 24 months ago by
pharamac
• 0
0
votes
1
reply
1.2k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 11 months ago by
Vanatta
• 0 • written 2.9 years ago by
mairah.khan
• 0
1
vote
2
replies
1.1k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
11 months ago
Levi
• 0
0
votes
2
replies
519
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
12 months ago
davca
• 0
0
votes
1
reply
733
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 12 months ago by
ATpoint
★ 4.5k • written 12 months ago by
ellen.francis
• 0
1
vote
1
reply
672
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 13 months ago by
tangming2005
▴ 200 • written 13 months ago by
meenae
▴ 10
0
votes
1
reply
573
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 15 months ago by
ATpoint
★ 4.5k • written 15 months ago by
jiecn
• 0
0
votes
1
reply
4.3k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 16 months ago by
James W. MacDonald
67k • written 16 months ago by
chiwut.wong
• 0
1
vote
1
reply
683
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 17 months ago by
ATpoint
★ 4.5k • written 17 months ago by
khaserdene99
• 0
0
votes
1
reply
928
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 17 months ago by
ATpoint
★ 4.5k • written 17 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.7k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 7 months ago by
Ashley
• 0 • written 17 months ago by
zxc741xb
• 0
3
votes
6
replies
1.1k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 17 months ago by
Gordon Smyth
51k • written 18 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
707
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 17 months ago by
Michael Love
42k • written 18 months ago by
suphamon.j
▴ 20
2
votes
1
reply
792
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 17 months ago by
andres.firrincieli
▴ 50 • written 18 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
567
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
18 months ago
Levi
• 0
3
votes
7
replies
1.7k
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
18 months ago
Ortega-C
▴ 10
0
votes
1
reply
671
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 18 months ago by
ATpoint
★ 4.5k • written 18 months ago by
Adam
• 0
0
votes
0
replies
710
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
19 months ago
Ortega-C
▴ 10
0
votes
2
replies
800
views
WGCNA problem
WGCNA
updated 19 months ago by
Ortega-C
▴ 10 • written 19 months ago by
mortezaali
• 0
0
votes
0
replies
721
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
19 months ago
Levi
• 0
0
votes
0
replies
589
views
Module Trait Corelation
WGCNA
20 months ago
allanokwaro
• 0
2
votes
3
replies
1.3k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 20 months ago by
ATpoint
★ 4.5k • written 20 months ago by
suphamon.j
▴ 20
0
votes
0
replies
633
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
21 months ago
Sooni
▴ 10
0
votes
0
replies
655
views
Multiple way network preservation
wgcna
21 months ago
madzayasodara
• 0
0
votes
0
replies
732
views
WGCNA TOM file empty
WGCNA
TOM
21 months ago
gianni.drm
• 0
0
votes
0
replies
1.1k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
21 months ago
gianni.drm
• 0
0
votes
1
reply
1.2k
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 8 months ago by
boczniak767
▴ 740 • written 21 months ago by
Kim
• 0
0
votes
1
reply
656
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 22 months ago by
andres.firrincieli
▴ 50 • written 22 months ago by
S
• 0
0
votes
0
replies
778
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
22 months ago
S
• 0
0
votes
0
replies
770
views
Problems running WGCNA
WGCNA
23 months ago
S
• 0
0
votes
0
replies
657
views
coexpression networks
WGCNA
igraph
24 months ago
María José
• 0
0
votes
0
replies
716
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
24 months ago
Abdullah
• 0
0
votes
0
replies
1.1k
views
WGCNA: minModuleSize is not responding correctly
Network
minModuleSize
WGCNA
wgcna
24 months ago • updated 7 weeks ago
bioinformaticssrm2011
• 0
2
votes
1
reply
991
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 2.2 years ago by
andres.firrincieli
▴ 50 • written 2.2 years ago by
ikumar2000
▴ 10
50 results • Page
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https://diendannhansu.com/threads/hayal-sohbet-odalari.667004/ https://forum.realdigital.org/u/serkan https://animefagos.com/miembros/ser…
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Comment: Is it recommended to analyze different tissues together when using edgeR
by
Gordon Smyth
51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data
by
Melisa Tecik
• 0
Thanks a lot for the help. You saved my day
Answer: Differene between the Wald and LRT test for time-series gene expression data
by
James W. MacDonald
67k
The advantage to using the LRT is that it's an omnibus test that tells you if there are changes at any time point. If you have lots of time…
Votes
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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Answer: Is it recommended to analyze different tissues together when using edgeR
Answer: Is it recommended to analyze different tissues together when using edgeR
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Gordon Smyth
51k
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• 0
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67k
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