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wgcna
•
reset
0
votes
0
replies
26
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
1 day ago
k200987
• 0
0
votes
2
replies
207
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
6 weeks ago
Gimena
• 0
0
votes
2
replies
238
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
7 weeks ago • updated 6 weeks ago
w.cookson
• 0
0
votes
1
reply
180
views
problem with ClusterRepro function
WGCNA
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
Antonio.Aubry
• 0
0
votes
1
reply
313
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Priya
• 0
0
votes
2
replies
557
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 5 months ago by
aehall26
• 0
4
votes
3
replies
1.0k
views
WGCNA documentation not available
WGCNA
written 5 months ago by
ramonmassoni
▴ 10
1
vote
2
replies
697
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
5 months ago • updated 4 months ago
Levi
• 0
0
votes
2
replies
320
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
1
reply
527
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 6 months ago by
ATpoint
★ 4.1k • written 6 months ago by
ellen.francis
• 0
1
vote
1
reply
424
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by
tangming2005
▴ 190 • written 6 months ago by
meenae
▴ 10
0
votes
1
reply
405
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 8 months ago by
ATpoint
★ 4.1k • written 9 months ago by
jiecn
• 0
0
votes
1
reply
2.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
chiwut.wong
• 0
1
vote
1
reply
507
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
khaserdene99
• 0
0
votes
1
reply
636
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 11 months ago by
ATpoint
★ 4.1k • written 11 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 29 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
3
votes
6
replies
858
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
488
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 11 months ago by
Michael Love
42k • written 11 months ago by
suphamon.j
▴ 20
2
votes
1
reply
523
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 11 months ago by
andres.firrincieli
▴ 50 • written 11 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
436
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
11 months ago
Levi
• 0
3
votes
7
replies
1.2k
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
12 months ago
Ortega-C
▴ 10
0
votes
1
reply
532
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 12 months ago by
ATpoint
★ 4.1k • written 12 months ago by
Adam
• 0
0
votes
0
replies
559
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
13 months ago • updated 12 months ago
Ortega-C
▴ 10
0
votes
2
replies
618
views
WGCNA problem
WGCNA
updated 12 months ago by
Ortega-C
▴ 10 • written 13 months ago by
mortezaali
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by
mauricio.microbiol
• 0
0
votes
0
replies
573
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
13 months ago
Levi
• 0
0
votes
0
replies
437
views
Module Trait Corelation
WGCNA
14 months ago
allanokwaro
• 0
2
votes
3
replies
928
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.1k • written 14 months ago by
suphamon.j
▴ 20
0
votes
0
replies
454
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
15 months ago
Sooni
▴ 10
0
votes
0
replies
489
views
Multiple way network preservation
wgcna
15 months ago
madzayasodara
• 0
0
votes
0
replies
543
views
WGCNA TOM file empty
WGCNA
TOM
15 months ago
gianni.drm
• 0
0
votes
0
replies
846
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
15 months ago
gianni.drm
• 0
0
votes
1
reply
896
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 10 weeks ago by
boczniak767
▴ 720 • written 15 months ago by
Kim
• 0
0
votes
1
reply
534
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 15 months ago by
andres.firrincieli
▴ 50 • written 15 months ago by
S
• 0
0
votes
0
replies
627
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
16 months ago
S
• 0
0
votes
0
replies
618
views
Problems running WGCNA
WGCNA
17 months ago
S
• 0
0
votes
0
replies
534
views
coexpression networks
WGCNA
igraph
17 months ago
María José
• 0
0
votes
0
replies
524
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
17 months ago
Abdullah
• 0
0
votes
2
replies
942
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 1 day ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
0
votes
0
replies
782
views
WGCNA: minModuleSize is not responding correctly
wgcna
Network
WGCNA
minModuleSize
18 months ago • updated 17 months ago
bioinformaticssrm2011
• 0
2
votes
1
reply
811
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 20 months ago by
andres.firrincieli
▴ 50 • written 20 months ago by
ikumar2000
▴ 10
0
votes
1
reply
834
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 20 months ago by
andres.firrincieli
▴ 50 • written 20 months ago by
Recep
▴ 20
0
votes
0
replies
568
views
MM-GS plot doesn't show any negative correlation
wgcna
21 months ago
shubhankar.pawar
• 0
0
votes
1
reply
971
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 22 months ago by
Cannabis Equipment Financing
• 0 • written 22 months ago by
803ebee7
• 0
0
votes
0
replies
641
views
ARACNe Sample Size
grndata
GRN
ARACNE
WGCNA
22 months ago
Harrsha
• 0
0
votes
0
replies
526
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
22 months ago
María José
• 0
0
votes
0
replies
619
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference
SampledBlockWiseModules
WGCNA
22 months ago
as8020
• 0
0
votes
0
replies
427
views
WGCNA consensusMEDdissimilrity
WGCNA
2.0 years ago
María José
• 0
1
vote
3
replies
1.8k
views
WGCNA error
WGCNA
2.0 years ago
ayabalbaa1990
• 0
0
votes
0
replies
773
views
The gene clusters from the WGCNA dendrogram output are not in order
Clustering
WGCNA
2.0 years ago
chiwut.wong
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
makala
• 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
by
Erik Wright
▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
Matthew Thornton
▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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42k
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