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WGCNA
•
reset
0
votes
2
replies
174
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
23 days ago • updated 22 days ago
Gimena
• 0
0
votes
2
replies
214
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
28 days ago • updated 23 days ago
w.cookson
• 0
0
votes
1
reply
162
views
problem with ClusterRepro function
WGCNA
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Antonio.Aubry
• 0
0
votes
1
reply
247
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 11 weeks ago by
ATpoint
★ 4.0k • written 11 weeks ago by
Priya
• 0
0
votes
2
replies
489
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by
aehall26
• 0
4
votes
3
replies
872
views
WGCNA documentation not available
WGCNA
written 4 months ago by
ramonmassoni
▴ 10
1
vote
2
replies
653
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
4 months ago
Levi
• 0
0
votes
2
replies
301
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
1
reply
480
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
ellen.francis
• 0
1
vote
1
reply
394
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
381
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
jiecn
• 0
0
votes
1
reply
1.8k
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
487
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
khaserdene99
• 0
0
votes
1
reply
593
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 8 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
3
votes
6
replies
832
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
462
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 10 months ago by
Michael Love
41k • written 11 months ago by
suphamon.j
▴ 20
2
votes
1
reply
499
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
417
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
11 months ago
Ortega-C
▴ 10
0
votes
1
reply
518
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 11 months ago by
ATpoint
★ 4.0k • written 11 months ago by
Adam
• 0
0
votes
0
replies
539
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
12 months ago
Ortega-C
▴ 10
0
votes
2
replies
600
views
WGCNA problem
WGCNA
updated 12 months ago by
Ortega-C
▴ 10 • written 12 months ago by
mortezaali
• 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
0
replies
557
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
12 months ago
Levi
• 0
0
votes
0
replies
410
views
Module Trait Corelation
WGCNA
13 months ago
allanokwaro
• 0
2
votes
3
replies
879
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
suphamon.j
▴ 20
0
votes
0
replies
432
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
14 months ago
Sooni
▴ 10
0
votes
0
replies
474
views
Multiple way network preservation
wgcna
14 months ago
madzayasodara
• 0
0
votes
0
replies
524
views
WGCNA TOM file empty
WGCNA
TOM
14 months ago
gianni.drm
• 0
0
votes
0
replies
805
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
14 months ago
gianni.drm
• 0
0
votes
1
reply
868
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 8 weeks ago by
boczniak767
▴ 720 • written 14 months ago by
Kim
• 0
0
votes
1
reply
516
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
615
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago
S
• 0
0
votes
0
replies
590
views
Problems running WGCNA
WGCNA
16 months ago
S
• 0
0
votes
0
replies
521
views
coexpression networks
WGCNA
igraph
17 months ago
María José
• 0
0
votes
0
replies
498
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
17 months ago
Abdullah
• 0
0
votes
1
reply
874
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 4 months ago by
janetdelvalle056
• 0 • written 17 months ago by
pharamac
• 0
0
votes
0
replies
739
views
WGCNA: minModuleSize is not responding correctly
wgcna
Network
WGCNA
minModuleSize
17 months ago
bioinformaticssrm2011
• 0
2
votes
1
reply
785
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 19 months ago by
andres.firrincieli
▴ 50 • written 19 months ago by
ikumar2000
▴ 10
0
votes
1
reply
807
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
555
views
MM-GS plot doesn't show any negative correlation
wgcna
21 months ago
shubhankar.pawar
• 0
0
votes
1
reply
946
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 21 months ago by
Cannabis Equipment Financing
• 0 • written 21 months ago by
803ebee7
• 0
0
votes
0
replies
626
views
ARACNe Sample Size
grndata
GRN
ARACNE
WGCNA
21 months ago
Harrsha
• 0
0
votes
0
replies
514
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
21 months ago
María José
• 0
0
votes
0
replies
606
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference
SampledBlockWiseModules
WGCNA
21 months ago
as8020
• 0
0
votes
0
replies
417
views
WGCNA consensusMEDdissimilrity
WGCNA
23 months ago
María José
• 0
1
vote
3
replies
1.7k
views
WGCNA error
WGCNA
24 months ago • updated 23 months ago
ayabalbaa1990
• 0
0
votes
0
replies
749
views
The gene clusters from the WGCNA dendrogram output are not in order
Clustering
WGCNA
24 months ago
chiwut.wong
• 0
0
votes
0
replies
648
views
FILTER GENES FOR WGCNA
WGCNA
24 months ago
María José
• 0
50 results • Page
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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• 0
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