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WGCNA
•
reset
6
votes
8
replies
5.0k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 5.1 years ago by
Colari19
▴ 60
0
votes
8
replies
3.8k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.1 years ago by
mauricio.microbiol
• 0
0
votes
1
reply
607
views
WGCNA
WGCNA
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.8k • written 5 weeks ago by
bioinformaticssrm2011
• 0
0
votes
1
reply
188
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 6 weeks ago by
dirty.cougar.risi
• 0 • written 6 weeks ago by
Μαρία
• 0
11
votes
6
replies
4.4k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 11 weeks ago by
Ivo
• 0 • written 8.7 years ago by
2323982403
▴ 60
0
votes
2
replies
445
views
WGCNA
WGCNA
Normalization
RNASeq
updated 12 weeks ago by
pammelala304
• 0 • written 12 weeks ago by
Vishnu
• 0
0
votes
1
reply
555
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 3 months ago by
ATpoint
★ 4.8k • written 3 months ago by
ddrummer0056
• 0
0
votes
1
reply
276
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 3 months ago by
ATpoint
★ 4.8k • written 3 months ago by
Reuben
• 0
0
votes
2
replies
295
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
3 months ago
Vinesh
• 0
0
votes
1
reply
179
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 3 months ago by
ATpoint
★ 4.8k • written 3 months ago by
Harshul
• 0
0
votes
1
reply
409
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 5 months ago by
ATpoint
★ 4.8k • written 5 months ago by
siobhan.dietz
• 0
0
votes
0
replies
266
views
WGCNA module preservation using only adjacency matrix
WGCNA
6 months ago
yang1641
• 0
3
votes
4
replies
1.2k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
7 months ago
sukeshinik5
▴ 20
1
vote
1
reply
654
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 7 months ago by
Lluís Revilla Sancho
▴ 760 • written 7 months ago by
Nasim
• 0
0
votes
0
replies
421
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
7 months ago
Fernanda
• 0
0
votes
1
reply
469
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 8 months ago by
Lluís Revilla Sancho
▴ 760 • written 8 months ago by
emilymily77
• 0
0
votes
1
reply
494
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
bioinformaticssrm2011
• 0
1
vote
3
replies
4.1k
views
WGNCA kME vs. kIM
WGCNA
updated 11 months ago by
Vitor
• 0 • written 9.7 years ago by
akridgerunner
▴ 30
0
votes
0
replies
384
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
12 months ago
k200987
• 0
0
votes
2
replies
670
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
13 months ago
Gimena
• 0
0
votes
2
replies
748
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
13 months ago
w.cookson
• 0
0
votes
1
reply
551
views
problem with ClusterRepro function
WGCNA
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
1.1k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 15 months ago by
ATpoint
★ 4.8k • written 15 months ago by
Priya
• 0
0
votes
2
replies
1.5k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 17 months ago by
aehall26
• 0
4
votes
3
replies
2.6k
views
WGCNA documentation not available
WGCNA
written 17 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
2.2k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 12 months ago by
mariakenneth147
• 0 • written 2.5 years ago by
pharamac
• 0
0
votes
1
reply
1.4k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 17 months ago by
Vanatta
• 0 • written 3.4 years ago by
mairah.khan
• 0
1
vote
2
replies
1.6k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
17 months ago • updated 16 months ago
Levi
• 0
0
votes
2
replies
638
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
18 months ago • updated 17 months ago
davca
• 0
0
votes
1
reply
877
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 18 months ago by
ATpoint
★ 4.8k • written 18 months ago by
ellen.francis
• 0
1
vote
2
replies
1.0k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 18 months ago by
meenae
▴ 10
0
votes
1
reply
715
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 21 months ago by
ATpoint
★ 4.8k • written 21 months ago by
jiecn
• 0
0
votes
1
reply
4.9k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
chiwut.wong
• 0
1
vote
1
reply
800
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 23 months ago by
ATpoint
★ 4.8k • written 23 months ago by
khaserdene99
• 0
0
votes
1
reply
1.2k
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 23 months ago by
ATpoint
★ 4.8k • written 23 months ago by
suphamon.j
▴ 20
2
votes
5
replies
2.0k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 13 months ago by
Ashley
• 0 • written 23 months ago by
zxc741xb
• 0
3
votes
6
replies
1.3k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 23 months ago by
Gordon Smyth
52k • written 23 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
878
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 23 months ago by
Michael Love
43k • written 24 months ago by
suphamon.j
▴ 20
2
votes
1
reply
967
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 23 months ago by
andres.firrincieli
▴ 50 • written 24 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
684
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
24 months ago
Levi
• 0
3
votes
7
replies
2.1k
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
2.0 years ago
Ortega-C
▴ 10
0
votes
1
reply
780
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.0 years ago by
ATpoint
★ 4.8k • written 2.0 years ago by
Adam
• 0
0
votes
0
replies
805
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
2.1 years ago
Ortega-C
▴ 10
0
votes
2
replies
931
views
WGCNA problem
WGCNA
updated 2.1 years ago by
Ortega-C
▴ 10 • written 2.1 years ago by
mortezaali
• 0
0
votes
0
replies
836
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.1 years ago
Levi
• 0
0
votes
0
replies
699
views
Module Trait Corelation
WGCNA
2.1 years ago
allanokwaro
• 0
2
votes
3
replies
1.5k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 2.1 years ago by
ATpoint
★ 4.8k • written 2.2 years ago by
suphamon.j
▴ 20
0
votes
0
replies
774
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
2.2 years ago
Sooni
▴ 10
0
votes
0
replies
766
views
Multiple way network preservation
wgcna
2.2 years ago
madzayasodara
• 0
0
votes
0
replies
832
views
WGCNA TOM file empty
WGCNA
TOM
2.3 years ago
gianni.drm
• 0
50 results • Page
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Recent ...
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Comment: DiffBind - question on the use of filtered or unfiltered input data
by
sloperun3az
• 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash
by
sloperun3az
• 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr
by
Paul Harrison
▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Gordon Smyth
52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Comment: limma::voom vs edgeR::voomLmFit - when to use?
by
Geoff
• 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Votes
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
parameters of filterByExpr
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