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wgcna
•
reset
0
votes
4
replies
5.5k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.8 years ago by
mauricio.microbiol
• 0
0
votes
1
reply
183
views
wgcna module preseravtion taking too long?
WGCNA
updated 17 days ago by
ATpoint
★ 5.0k • written 23 days ago by
lamia11me
• 0
1
vote
2
replies
382
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 5 months ago by
A.Barden
▴ 20
0
votes
4
replies
726
views
Issue with Soft-Thresholding in WGCNA
WGCNA
written 9 months ago by
Μαρία
• 0
3
votes
4
replies
8.2k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.4 years ago by
Arindam
▴ 80
0
votes
5
replies
950
views
WGCNA
WGCNA
Normalization
RNASeq
written 10 months ago by
Vishnu
• 0
6
votes
8
replies
5.8k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 5.7 years ago by
Colari19
▴ 60
0
votes
1
reply
962
views
WGCNA
WGCNA
DESeq2
updated 9 months ago by
ATpoint
★ 5.0k • written 9 months ago by
bioinformaticssrm2011
• 0
11
votes
6
replies
4.8k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 10 months ago by
Ivo
• 0 • written 9.4 years ago by
2323982403
▴ 60
0
votes
1
reply
824
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
ddrummer0056
• 0
0
votes
1
reply
650
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Reuben
• 0
0
votes
2
replies
606
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
11 months ago
Vinesh
• 0
0
votes
1
reply
372
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
Harshul
• 0
0
votes
1
reply
768
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
siobhan.dietz
• 0
0
votes
0
replies
495
views
WGCNA module preservation using only adjacency matrix
WGCNA
14 months ago
yang1641
• 0
3
votes
4
replies
1.7k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
15 months ago
sukeshinik5
▴ 20
1
vote
1
reply
1.0k
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 15 months ago by
Lluís Revilla Sancho
▴ 760 • written 15 months ago by
Nasim
• 0
0
votes
0
replies
633
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
15 months ago
Fernanda
• 0
0
votes
1
reply
676
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 16 months ago by
Lluís Revilla Sancho
▴ 760 • written 16 months ago by
emilymily77
• 0
0
votes
1
reply
699
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 16 months ago by
James W. MacDonald
68k • written 16 months ago by
bioinformaticssrm2011
• 0
1
vote
3
replies
4.6k
views
WGNCA kME vs. kIM
WGCNA
updated 19 months ago by
Vitor
• 0 • written 10.3 years ago by
akridgerunner
▴ 30
0
votes
0
replies
560
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
20 months ago
k200987
• 0
0
votes
2
replies
929
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
21 months ago
Gimena
• 0
0
votes
2
replies
1.0k
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
21 months ago
w.cookson
• 0
0
votes
1
reply
728
views
problem with ClusterRepro function
WGCNA
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
1.4k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
Priya
• 0
0
votes
2
replies
1.8k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 2.1 years ago by
aehall26
• 0
4
votes
3
replies
3.1k
views
WGCNA documentation not available
WGCNA
written 2.1 years ago by
ramonmassoni
▴ 10
0
votes
2
replies
2.6k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 20 months ago by
mariakenneth147
• 0 • written 3.1 years ago by
pharamac
• 0
0
votes
1
reply
1.7k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 2.1 years ago by
Vanatta
• 0 • written 4.1 years ago by
mairah.khan
• 0
1
vote
2
replies
1.9k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
2.1 years ago • updated 2.0 years ago
Levi
• 0
0
votes
2
replies
859
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
2.1 years ago
davca
• 0
0
votes
1
reply
1.1k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.2 years ago by
ATpoint
★ 5.0k • written 2.2 years ago by
ellen.francis
• 0
1
vote
2
replies
1.3k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.2 years ago by
meenae
▴ 10
0
votes
1
reply
874
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
jiecn
• 0
0
votes
1
reply
5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
chiwut.wong
• 0
1
vote
1
reply
976
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
khaserdene99
• 0
0
votes
1
reply
1.5k
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
suphamon.j
▴ 20
2
votes
5
replies
2.4k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 21 months ago by
Ashley
• 0 • written 2.6 years ago by
zxc741xb
• 0
3
votes
6
replies
1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 2.6 years ago by
Gordon Smyth
53k • written 2.6 years ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
1.1k
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
suphamon.j
▴ 20
2
votes
1
reply
1.2k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 2.6 years ago by
andres.firrincieli
▴ 50 • written 2.6 years ago by
hesse.sebastian
▴ 10
0
votes
0
replies
846
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
2.6 years ago
Levi
• 0
3
votes
7
replies
2.6k
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
2.7 years ago
Ortega-C
▴ 10
0
votes
1
reply
930
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
Adam
• 0
0
votes
0
replies
1.0k
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
2.7 years ago
Ortega-C
▴ 10
0
votes
2
replies
1.2k
views
WGCNA problem
WGCNA
updated 2.7 years ago by
Ortega-C
▴ 10 • written 2.7 years ago by
mortezaali
• 0
0
votes
0
replies
1.0k
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.8 years ago
Levi
• 0
0
votes
0
replies
825
views
Module Trait Corelation
WGCNA
2.8 years ago
allanokwaro
• 0
2
votes
3
replies
1.9k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
suphamon.j
▴ 20
336 results • Page
1 of 7
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Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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