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wgcna
•
reset
0
votes
2
replies
352
views
wgcna module preseravtion taking too long?
WGCNA
written 10 weeks ago by
lamia11me
• 0
1
vote
2
replies
446
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 6 months ago by
A.Barden
▴ 20
0
votes
1
reply
1.1k
views
WGCNA
WGCNA
DESeq2
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
bioinformaticssrm2011
• 0
0
votes
4
replies
878
views
Issue with Soft-Thresholding in WGCNA
WGCNA
written 11 months ago by
Μαρία
• 0
0
votes
5
replies
1.1k
views
WGCNA
WGCNA
Normalization
RNASeq
written 12 months ago by
Vishnu
• 0
0
votes
1
reply
961
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
ddrummer0056
• 0
0
votes
1
reply
393
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Harshul
• 0
0
votes
2
replies
719
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
13 months ago
Vinesh
• 0
0
votes
1
reply
780
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Reuben
• 0
0
votes
1
reply
844
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 15 months ago by
ATpoint
★ 5.0k • written 15 months ago by
siobhan.dietz
• 0
0
votes
0
replies
569
views
WGCNA module preservation using only adjacency matrix
WGCNA
15 months ago
yang1641
• 0
3
votes
4
replies
1.9k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
16 months ago
sukeshinik5
▴ 20
1
vote
1
reply
1.0k
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 16 months ago by
Lluís Revilla Sancho
▴ 760 • written 16 months ago by
Nasim
• 0
0
votes
0
replies
679
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
17 months ago
Fernanda
• 0
0
votes
1
reply
842
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 17 months ago by
Lluís Revilla Sancho
▴ 760 • written 17 months ago by
emilymily77
• 0
0
votes
1
reply
812
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
bioinformaticssrm2011
• 0
0
votes
0
replies
605
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
21 months ago
k200987
• 0
0
votes
2
replies
1.0k
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
23 months ago
Gimena
• 0
0
votes
2
replies
1.1k
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
23 months ago
w.cookson
• 0
0
votes
1
reply
760
views
problem with ClusterRepro function
WGCNA
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
1.4k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years 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 2.2 years ago by
aehall26
• 0
4
votes
3
replies
3.3k
views
WGCNA documentation not available
WGCNA
written 2.2 years ago by
ramonmassoni
▴ 10
1
vote
2
replies
2.1k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
2.2 years ago
Levi
• 0
0
votes
2
replies
892
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
2.3 years ago
davca
• 0
0
votes
1
reply
1.1k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
ellen.francis
• 0
1
vote
2
replies
1.4k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.3 years ago by
meenae
▴ 10
0
votes
1
reply
913
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
jiecn
• 0
0
votes
1
reply
5.2k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 2.6 years ago by
James W. MacDonald
68k • written 2.6 years ago by
chiwut.wong
• 0
1
vote
1
reply
1.0k
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
khaserdene99
• 0
0
votes
1
reply
1.6k
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
suphamon.j
▴ 20
2
votes
5
replies
2.5k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 22 months ago by
Ashley
• 0 • written 2.7 years ago by
zxc741xb
• 0
3
votes
6
replies
1.7k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 2.7 years ago by
Gordon Smyth
53k • written 2.8 years ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
1.1k
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 2.7 years ago by
Michael Love
43k • written 2.8 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 2.7 years ago by
andres.firrincieli
▴ 50 • written 2.8 years ago by
hesse.sebastian
▴ 10
0
votes
0
replies
890
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
2.8 years ago
Levi
• 0
3
votes
7
replies
2.8k
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
2.8 years ago
Ortega-C
▴ 10
0
votes
1
reply
957
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.8 years ago by
ATpoint
★ 5.0k • written 2.8 years ago by
Adam
• 0
0
votes
0
replies
1.1k
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
2.9 years ago • updated 2.8 years ago
Ortega-C
▴ 10
0
votes
2
replies
1.2k
views
WGCNA problem
WGCNA
updated 2.8 years ago by
Ortega-C
▴ 10 • written 2.9 years ago by
mortezaali
• 0
0
votes
4
replies
5.8k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.9 years ago by
mauricio.microbiol
• 0
0
votes
0
replies
1.1k
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.9 years ago
Levi
• 0
0
votes
0
replies
855
views
Module Trait Corelation
WGCNA
2.9 years ago
allanokwaro
• 0
2
votes
3
replies
2.0k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 2.9 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
suphamon.j
▴ 20
0
votes
0
replies
982
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
3.0 years ago
Sooni
▴ 10
0
votes
0
replies
925
views
Multiple way network preservation
wgcna
3.0 years ago
madzayasodara
• 0
0
votes
0
replies
1.0k
views
WGCNA TOM file empty
WGCNA
TOM
3.1 years ago
gianni.drm
• 0
0
votes
0
replies
1.7k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
3.1 years ago
gianni.drm
• 0
0
votes
1
reply
1.7k
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 24 months ago by
boczniak767
▴ 740 • written 3.1 years ago by
Kim
• 0
0
votes
1
reply
909
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 3.1 years ago by
andres.firrincieli
▴ 50 • written 3.1 years ago by
S
• 0
336 results • Page
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Comment: Can sample-level weights be used when analysing GSVA scores in limma?
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A.Barden
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Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions
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Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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