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WGCNA
•
reset
0
votes
0
replies
31
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
1 day ago
k200987
• 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
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
241
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
182
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
317
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
558
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
0
votes
2
replies
946
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 2 days ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
0
votes
1
reply
1.0k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 5 months ago by
Vanatta
• 0 • written 2.4 years ago by
mairah.khan
• 0
1
vote
2
replies
698
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
323
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
1
reply
528
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
425
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
406
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 9 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
508
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
640
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 4 weeks ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
3
votes
6
replies
860
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
490
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
525
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
438
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
11 months ago
Levi
• 0
1
vote
2
replies
2.7k
views
WGNCA kME vs. kIM
WGCNA
updated 12 months ago by
brukti
• 0 • written 8.7 years ago by
akridgerunner
▴ 30
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
534
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
560
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
619
views
WGCNA problem
WGCNA
updated 12 months ago by
Ortega-C
▴ 10 • written 13 months ago by
mortezaali
• 0
0
votes
0
replies
575
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
13 months ago
Levi
• 0
0
votes
0
replies
439
views
Module Trait Corelation
WGCNA
14 months ago
allanokwaro
• 0
2
votes
3
replies
930
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 14 months ago by
ATpoint
★ 4.1k • written 14 months ago by
suphamon.j
▴ 20
0
votes
0
replies
456
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
15 months ago
Sooni
▴ 10
0
votes
0
replies
491
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
848
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
15 months ago
gianni.drm
• 0
0
votes
1
reply
900
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 11 weeks ago by
boczniak767
▴ 720 • written 15 months ago by
Kim
• 0
0
votes
1
reply
536
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
630
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
16 months ago
S
• 0
0
votes
0
replies
621
views
Problems running WGCNA
WGCNA
17 months ago
S
• 0
0
votes
0
replies
535
views
coexpression networks
WGCNA
igraph
17 months ago
María José
• 0
0
votes
0
replies
525
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
17 months ago
Abdullah
• 0
0
votes
0
replies
786
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
836
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
569
views
MM-GS plot doesn't show any negative correlation
wgcna
21 months ago
shubhankar.pawar
• 0
0
votes
1
reply
974
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
642
views
ARACNe Sample Size
grndata
GRN
ARACNE
WGCNA
22 months ago
Harrsha
• 0
0
votes
0
replies
527
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
22 months ago
María José
• 0
0
votes
0
replies
620
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference
SampledBlockWiseModules
WGCNA
22 months ago
as8020
• 0
0
votes
0
replies
428
views
WGCNA consensusMEDdissimilrity
WGCNA
2.0 years ago
María José
• 0
50 results • Page
1 of 1
Recent ...
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Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network()
by
ninidea
• 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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
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