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WGCNA
•
reset
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago
Gimena
• 0
0
votes
2
replies
226
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
5 weeks ago • updated 4 weeks ago
w.cookson
• 0
0
votes
1
reply
168
views
problem with ClusterRepro function
WGCNA
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
Antonio.Aubry
• 0
0
votes
1
reply
266
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 12 weeks ago by
ATpoint
★ 4.1k • written 12 weeks ago by
Priya
• 0
0
votes
2
replies
514
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
915
views
WGCNA documentation not available
WGCNA
written 4 months ago by
ramonmassoni
▴ 10
0
votes
1
reply
892
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
1
reply
996
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 4 months ago by
Vanatta
• 0 • written 2.4 years ago by
mairah.khan
• 0
1
vote
2
replies
664
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
312
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
1
reply
491
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
ellen.francis
• 0
1
vote
1
reply
402
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
387
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
jiecn
• 0
0
votes
1
reply
2.0k
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
494
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
605
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 15 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
3
votes
6
replies
838
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
470
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 11 months ago by
Michael Love
41k • written 11 months ago by
suphamon.j
▴ 20
2
votes
1
reply
506
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
426
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 11 months ago by
brukti
• 0 • written 8.6 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
11 months ago
Ortega-C
▴ 10
0
votes
1
reply
521
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
547
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
606
views
WGCNA problem
WGCNA
updated 12 months ago by
Ortega-C
▴ 10 • written 12 months ago by
mortezaali
• 0
0
votes
0
replies
565
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
13 months ago
Levi
• 0
0
votes
0
replies
419
views
Module Trait Corelation
WGCNA
13 months ago
allanokwaro
• 0
2
votes
3
replies
892
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
suphamon.j
▴ 20
0
votes
0
replies
440
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
14 months ago
Sooni
▴ 10
0
votes
0
replies
485
views
Multiple way network preservation
wgcna
14 months ago
madzayasodara
• 0
0
votes
0
replies
530
views
WGCNA TOM file empty
WGCNA
TOM
14 months ago
gianni.drm
• 0
0
votes
0
replies
815
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
15 months ago
gianni.drm
• 0
0
votes
1
reply
877
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 8 weeks ago by
boczniak767
▴ 720 • written 15 months ago by
Kim
• 0
0
votes
1
reply
528
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
620
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago
S
• 0
0
votes
0
replies
599
views
Problems running WGCNA
WGCNA
16 months ago
S
• 0
0
votes
0
replies
526
views
coexpression networks
WGCNA
igraph
17 months ago
María José
• 0
0
votes
0
replies
504
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
17 months ago
Abdullah
• 0
0
votes
0
replies
753
views
WGCNA: minModuleSize is not responding correctly
wgcna
Network
WGCNA
minModuleSize
17 months ago
bioinformaticssrm2011
• 0
2
votes
1
reply
793
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
822
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
560
views
MM-GS plot doesn't show any negative correlation
wgcna
21 months ago
shubhankar.pawar
• 0
0
votes
1
reply
960
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
633
views
ARACNe Sample Size
grndata
GRN
ARACNE
WGCNA
22 months ago
Harrsha
• 0
0
votes
0
replies
520
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
22 months ago
María José
• 0
0
votes
0
replies
612
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference
SampledBlockWiseModules
WGCNA
22 months ago
as8020
• 0
0
votes
0
replies
419
views
WGCNA consensusMEDdissimilrity
WGCNA
24 months ago
María José
• 0
1
vote
3
replies
1.8k
views
WGCNA error
WGCNA
24 months ago
ayabalbaa1990
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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