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WGCNA
•
reset
0
votes
6
replies
2.1k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 15 months ago by
mauricio.microbiol
• 0
1
vote
3
replies
3.0k
views
WGNCA kME vs. kIM
WGCNA
updated 9 weeks ago by
Vitor
• 0 • written 8.9 years ago by
akridgerunner
▴ 30
0
votes
0
replies
137
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
10 weeks ago
k200987
• 0
0
votes
2
replies
315
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
3 months ago
Gimena
• 0
0
votes
2
replies
341
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
4 months ago • updated 3 months ago
w.cookson
• 0
0
votes
1
reply
253
views
problem with ClusterRepro function
WGCNA
updated 4 months ago by
James W. MacDonald
66k • written 4 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
444
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 5 months ago by
ATpoint
★ 4.2k • written 5 months ago by
Priya
• 0
0
votes
2
replies
719
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 7 months ago by
aehall26
• 0
4
votes
3
replies
1.3k
views
WGCNA documentation not available
WGCNA
written 7 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
1.1k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 10 weeks ago by
mariakenneth147
• 0 • written 20 months ago by
pharamac
• 0
0
votes
1
reply
1.1k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 7 months ago by
Vanatta
• 0 • written 2.6 years ago by
mairah.khan
• 0
1
vote
2
replies
857
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
8 months ago • updated 7 months ago
Levi
• 0
0
votes
2
replies
409
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
8 months ago
davca
• 0
0
votes
1
reply
607
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 8 months ago by
ATpoint
★ 4.2k • written 8 months ago by
ellen.francis
• 0
1
vote
1
reply
516
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 9 months ago by
tangming2005
▴ 190 • written 9 months ago by
meenae
▴ 10
0
votes
1
reply
458
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 11 months ago by
ATpoint
★ 4.2k • written 11 months ago by
jiecn
• 0
0
votes
1
reply
2.8k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 12 months ago by
James W. MacDonald
66k • written 12 months ago by
chiwut.wong
• 0
1
vote
1
reply
579
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 13 months ago by
ATpoint
★ 4.2k • written 13 months ago by
khaserdene99
• 0
0
votes
1
reply
750
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 13 months ago by
ATpoint
★ 4.2k • written 13 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.4k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 3 months ago by
Ashley
• 0 • written 13 months ago by
zxc741xb
• 0
3
votes
6
replies
964
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 14 months ago by
Gordon Smyth
51k • written 14 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
574
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 13 months ago by
Michael Love
42k • written 14 months ago by
suphamon.j
▴ 20
2
votes
1
reply
616
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 14 months ago by
andres.firrincieli
▴ 50 • written 14 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
485
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
14 months ago
Levi
• 0
3
votes
7
replies
1.4k
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
14 months ago
Ortega-C
▴ 10
0
votes
1
reply
581
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 15 months ago by
ATpoint
★ 4.2k • written 15 months ago by
Adam
• 0
0
votes
0
replies
607
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
15 months ago
Ortega-C
▴ 10
0
votes
2
replies
684
views
WGCNA problem
WGCNA
updated 15 months ago by
Ortega-C
▴ 10 • written 15 months ago by
mortezaali
• 0
0
votes
0
replies
630
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
15 months ago
Levi
• 0
0
votes
0
replies
509
views
Module Trait Corelation
WGCNA
16 months ago
allanokwaro
• 0
2
votes
3
replies
1.1k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 16 months ago by
ATpoint
★ 4.2k • written 16 months ago by
suphamon.j
▴ 20
0
votes
0
replies
519
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
17 months ago
Sooni
▴ 10
0
votes
0
replies
543
views
Multiple way network preservation
wgcna
17 months ago
madzayasodara
• 0
0
votes
0
replies
632
views
WGCNA TOM file empty
WGCNA
TOM
17 months ago
gianni.drm
• 0
0
votes
0
replies
952
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
17 months ago
gianni.drm
• 0
0
votes
1
reply
1.0k
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 4 months ago by
boczniak767
▴ 740 • written 17 months ago by
Kim
• 0
0
votes
1
reply
582
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 18 months ago by
andres.firrincieli
▴ 50 • written 18 months ago by
S
• 0
0
votes
0
replies
675
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
18 months ago
S
• 0
0
votes
0
replies
689
views
Problems running WGCNA
WGCNA
19 months ago
S
• 0
0
votes
0
replies
591
views
coexpression networks
WGCNA
igraph
20 months ago
María José
• 0
0
votes
0
replies
594
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
20 months ago
Abdullah
• 0
0
votes
0
replies
891
views
WGCNA: minModuleSize is not responding correctly
wgcna
Network
WGCNA
minModuleSize
20 months ago
bioinformaticssrm2011
• 0
2
votes
1
reply
876
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 22 months ago by
andres.firrincieli
▴ 50 • written 22 months ago by
ikumar2000
▴ 10
0
votes
1
reply
928
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 23 months ago by
andres.firrincieli
▴ 50 • written 23 months ago by
Recep
▴ 20
0
votes
0
replies
628
views
MM-GS plot doesn't show any negative correlation
wgcna
24 months ago
shubhankar.pawar
• 0
0
votes
1
reply
1.1k
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 2.0 years ago by
Cannabis Equipment Financing
• 0 • written 2.0 years ago by
803ebee7
• 0
0
votes
0
replies
686
views
ARACNe Sample Size
grndata
GRN
ARACNE
WGCNA
2.0 years ago
Harrsha
• 0
0
votes
0
replies
566
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
2.1 years ago
María José
• 0
0
votes
0
replies
667
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference
SampledBlockWiseModules
WGCNA
2.1 years ago
as8020
• 0
0
votes
0
replies
473
views
WGCNA consensusMEDdissimilrity
WGCNA
2.2 years ago
María José
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
Awards
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Popular Question
to
Lluís Revilla Sancho
▴ 730
Popular Question
to
maltethodberg
▴ 180
Scholar
to
Michael Love
42k
Popular Question
to
Leonardo Collado Torres
★ 1.1k
Scholar
to
Gordon Smyth
51k
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