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wgcna
•
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0
votes
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replies
62
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
6 days ago
k200987
• 0
0
votes
2
replies
962
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 7 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 4 weeks ago by
Garrett
• 0 • written 9.2 years ago by
brohawndg
▴ 150
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 5 weeks ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 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
209
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
7 weeks ago • updated 6 weeks ago
Gimena
• 0
0
votes
2
replies
246
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
7 weeks ago
w.cookson
• 0
0
votes
1
reply
186
views
problem with ClusterRepro function
WGCNA
updated 9 weeks ago by
James W. MacDonald
66k • written 9 weeks ago by
Antonio.Aubry
• 0
0
votes
1
reply
903
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
325
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
Priya
• 0
0
votes
1
reply
1.1k
views
WGCNA Preservation error
preservation
WGCNA
updated 4 months ago by
Gail
• 0 • written 2.4 years ago by
Sara
• 0
0
votes
2
replies
830
views
Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA
Module Detection
updated 4 months ago by
dima11i
• 0 • written 4.6 years ago by
vsa1111
• 0
1
vote
2
replies
703
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
563
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 5 months ago by
aehall26
• 0
5
votes
8
replies
4.0k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
0
votes
2
replies
1.4k
views
WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna
WGCNA
written 2.1 years ago by
bioinformaticssrm2011
• 0
4
votes
3
replies
1.0k
views
WGCNA documentation not available
WGCNA
written 5 months ago by
ramonmassoni
▴ 10
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
0
votes
2
replies
329
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
6 months ago
davca
• 0
0
votes
1
reply
531
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
428
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
409
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 10 months ago by
James W. MacDonald
66k • written 10 months ago by
chiwut.wong
• 0
6
votes
6
replies
2.8k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.1 years ago by
Colari19
▴ 60
1
vote
1
reply
509
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 11 months ago by
ATpoint
★ 4.1k • written 11 months ago by
khaserdene99
• 0
0
votes
1
reply
647
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
1
vote
0
replies
495
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 11 months ago by
Michael Love
42k • written 12 months ago by
suphamon.j
▴ 20
3
votes
6
replies
864
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
2
votes
1
reply
530
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 12 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
443
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
12 months ago
Levi
• 0
30 results • Page
1 of 1
Recent ...
Replies
Comment: Slightly different count plots from R and spreadsheet
by
ATpoint
★ 4.1k
I don't think it is the purpose of the support site to debug Excel behaviour. The issue might be how it combines replicates into a single v…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
Karosham.Reddy
• 0
Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?
Comment: recount3 problem downloading data from source sra
by
PABLO ANTONIO
• 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working
by
websterdelacruz2087055
• 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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Mike Smith
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mohammedtoufiq91
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