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wgcna
•
reset
1
vote
2
replies
334
views
Can limma be used with module eigengenes instead of genes?
limma
WGCNA
GSVA
written 3 months ago by
A.Barden
▴ 10
0
votes
4
replies
655
views
Issue with Soft-Thresholding in WGCNA
WGCNA
written 8 months ago by
Μαρία
• 0
3
votes
4
replies
8.0k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.3 years ago by
Arindam
▴ 80
0
votes
5
replies
887
views
WGCNA
WGCNA
Normalization
RNASeq
written 9 months ago by
Vishnu
• 0
6
votes
8
replies
5.6k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 5.6 years ago by
Colari19
▴ 60
0
votes
2
replies
5.2k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 4 months ago by
quordle
• 0 • written 2.7 years ago by
mauricio.microbiol
• 0
0
votes
1
reply
900
views
WGCNA
WGCNA
DESeq2
updated 7 months ago by
ATpoint
★ 5.0k • written 7 months ago by
bioinformaticssrm2011
• 0
11
votes
6
replies
4.8k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 9 months ago by
Ivo
• 0 • written 9.3 years ago by
2323982403
▴ 60
0
votes
1
reply
755
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA
pickSoftThreshold
SignedNowick
updated 9 months ago by
ATpoint
★ 5.0k • written 10 months ago by
ddrummer0056
• 0
0
votes
1
reply
578
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
Reuben
• 0
0
votes
2
replies
533
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis
RNA-seqdata
Powerselection
WGCNA
10 months ago
Vinesh
• 0
0
votes
1
reply
338
views
Ph.D. scholar
WGCNA
DataNormalization
MicroarrayData
updated 10 months ago by
ATpoint
★ 5.0k • written 10 months ago by
Harshul
• 0
0
votes
1
reply
700
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
siobhan.dietz
• 0
0
votes
0
replies
450
views
WGCNA module preservation using only adjacency matrix
WGCNA
12 months ago
yang1641
• 0
3
votes
4
replies
1.5k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
13 months ago
sukeshinik5
▴ 20
1
vote
1
reply
981
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 14 months ago by
Lluís Revilla Sancho
▴ 760 • written 14 months ago by
Nasim
• 0
0
votes
0
replies
600
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
14 months ago
Fernanda
• 0
0
votes
1
reply
628
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 14 months ago by
Lluís Revilla Sancho
▴ 760 • written 14 months ago by
emilymily77
• 0
0
votes
1
reply
657
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 14 months ago by
James W. MacDonald
68k • written 15 months ago by
bioinformaticssrm2011
• 0
1
vote
3
replies
4.4k
views
WGNCA kME vs. kIM
WGCNA
updated 18 months ago by
Vitor
• 0 • written 10.2 years ago by
akridgerunner
▴ 30
0
votes
0
replies
528
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
18 months ago
k200987
• 0
0
votes
2
replies
880
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
20 months ago
Gimena
• 0
0
votes
2
replies
964
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
20 months ago
w.cookson
• 0
0
votes
1
reply
694
views
problem with ClusterRepro function
WGCNA
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
1.3k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 22 months ago by
ATpoint
★ 5.0k • written 22 months ago by
Priya
• 0
0
votes
2
replies
1.7k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 24 months ago by
aehall26
• 0
4
votes
3
replies
3.1k
views
WGCNA documentation not available
WGCNA
written 24 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
2.5k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 18 months ago by
mariakenneth147
• 0 • written 3.0 years ago by
pharamac
• 0
0
votes
1
reply
1.6k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 24 months ago by
Vanatta
• 0 • written 4.0 years ago by
mairah.khan
• 0
1
vote
2
replies
1.8k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
2.0 years ago • updated 23 months ago
Levi
• 0
0
votes
2
replies
804
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
2.0 years ago
davca
• 0
0
votes
1
reply
1.0k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 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 2.1 years ago by
meenae
▴ 10
0
votes
1
reply
844
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 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 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
chiwut.wong
• 0
1
vote
1
reply
951
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
khaserdene99
• 0
0
votes
1
reply
1.4k
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
suphamon.j
▴ 20
2
votes
5
replies
2.3k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 19 months ago by
Ashley
• 0 • written 2.5 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 2.5 years ago by
Gordon Smyth
53k • written 2.5 years ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
1.0k
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 2.5 years ago by
Michael Love
43k • written 2.5 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 2.5 years ago by
andres.firrincieli
▴ 50 • written 2.5 years ago by
hesse.sebastian
▴ 10
0
votes
0
replies
810
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
2.5 years ago
Levi
• 0
3
votes
7
replies
2.5k
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
2.6 years ago
Ortega-C
▴ 10
0
votes
1
reply
902
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.6 years ago by
ATpoint
★ 5.0k • written 2.6 years ago by
Adam
• 0
0
votes
0
replies
971
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
2.6 years ago
Ortega-C
▴ 10
0
votes
2
replies
1.1k
views
WGCNA problem
WGCNA
updated 2.6 years ago by
Ortega-C
▴ 10 • written 2.6 years ago by
mortezaali
• 0
0
votes
0
replies
970
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
2.7 years ago
Levi
• 0
0
votes
0
replies
803
views
Module Trait Corelation
WGCNA
2.7 years ago
allanokwaro
• 0
2
votes
3
replies
1.8k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 2.7 years ago by
ATpoint
★ 5.0k • written 2.7 years ago by
suphamon.j
▴ 20
0
votes
0
replies
902
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
2.8 years ago
Sooni
▴ 10
335 results • Page
1 of 7
Recent ...
Replies
Comment: GOseq Probability Weight Function bad fit
by
ejasge.r.m
• 0
When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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