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WGCNA
•
reset
3
votes
4
replies
362
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
22 days ago
sukeshinik5
▴ 20
1
vote
1
reply
225
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 28 days ago by
Lluís Revilla Sancho
▴ 760 • written 28 days ago by
Nasim
• 0
0
votes
0
replies
157
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
6 weeks ago
Fernanda
• 0
0
votes
1
reply
239
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 7 weeks ago by
Lluís Revilla Sancho
▴ 760 • written 7 weeks ago by
emilymily77
• 0
0
votes
1
reply
244
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 7 weeks ago by
James W. MacDonald
67k • written 8 weeks ago by
bioinformaticssrm2011
• 0
0
votes
6
replies
2.5k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 19 months ago by
mauricio.microbiol
• 0
1
vote
3
replies
3.3k
views
WGNCA kME vs. kIM
WGCNA
updated 5 months ago by
Vitor
• 0 • written 9.1 years ago by
akridgerunner
▴ 30
0
votes
0
replies
234
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
5 months ago
k200987
• 0
0
votes
2
replies
451
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
7 months ago
Gimena
• 0
0
votes
2
replies
524
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
7 months ago
w.cookson
• 0
0
votes
1
reply
367
views
problem with ClusterRepro function
WGCNA
updated 7 months ago by
James W. MacDonald
67k • written 7 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
697
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
986
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
1.8k
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 5 months ago by
mariakenneth147
• 0 • written 23 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 • updated 10 months ago
Levi
• 0
0
votes
2
replies
509
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
11 months ago
davca
• 0
0
votes
1
reply
717
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 11 months ago by
ATpoint
★ 4.5k • written 11 months ago by
ellen.francis
• 0
1
vote
1
reply
651
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 12 months ago by
tangming2005
▴ 200 • written 12 months ago by
meenae
▴ 10
0
votes
1
reply
566
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 14 months ago by
ATpoint
★ 4.5k • written 14 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 15 months ago by
James W. MacDonald
67k • written 15 months ago by
chiwut.wong
• 0
1
vote
1
reply
677
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 16 months ago by
ATpoint
★ 4.5k • written 16 months ago by
khaserdene99
• 0
0
votes
1
reply
910
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 16 months ago by
ATpoint
★ 4.5k • written 16 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.6k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 6 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 17 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
697
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 17 months ago by
Michael Love
42k • written 17 months ago by
suphamon.j
▴ 20
2
votes
1
reply
771
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 17 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
556
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
17 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 • updated 17 months ago
Ortega-C
▴ 10
0
votes
1
reply
659
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
700
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
18 months ago
Ortega-C
▴ 10
0
votes
2
replies
788
views
WGCNA problem
WGCNA
updated 18 months ago by
Ortega-C
▴ 10 • written 18 months ago by
mortezaali
• 0
0
votes
0
replies
709
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
19 months ago
Levi
• 0
0
votes
0
replies
579
views
Module Trait Corelation
WGCNA
19 months ago
allanokwaro
• 0
2
votes
3
replies
1.2k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 19 months ago by
ATpoint
★ 4.5k • written 20 months ago by
suphamon.j
▴ 20
0
votes
0
replies
623
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
20 months ago
Sooni
▴ 10
0
votes
0
replies
640
views
Multiple way network preservation
wgcna
20 months ago
madzayasodara
• 0
0
votes
0
replies
723
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
647
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 21 months ago by
andres.firrincieli
▴ 50 • written 21 months ago by
S
• 0
0
votes
0
replies
765
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
21 months ago
S
• 0
0
votes
0
replies
760
views
Problems running WGCNA
WGCNA
22 months ago
S
• 0
0
votes
0
replies
649
views
coexpression networks
WGCNA
igraph
23 months ago
María José
• 0
0
votes
0
replies
704
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
23 months ago
Abdullah
• 0
0
votes
0
replies
1.0k
views
WGCNA: minModuleSize is not responding correctly
Network
minModuleSize
WGCNA
wgcna
23 months ago • updated 5 weeks ago
bioinformaticssrm2011
• 0
2
votes
1
reply
983
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 2.1 years ago by
andres.firrincieli
▴ 50 • written 2.1 years ago by
ikumar2000
▴ 10
0
votes
1
reply
1.1k
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 2.2 years ago by
andres.firrincieli
▴ 50 • written 2.2 years ago by
Recep
▴ 20
0
votes
0
replies
694
views
MM-GS plot doesn't show any negative correlation
wgcna
2.3 years ago
shubhankar.pawar
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
by
Ai
• 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2
by
icecreamlover
• 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
James W. MacDonald
67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
James W. MacDonald
67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
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Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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★ 1.5k
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51k
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