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wgcna
•
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0
votes
2
replies
202
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
6 weeks ago
Gimena
• 0
0
votes
2
replies
236
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
6 weeks ago
w.cookson
• 0
0
votes
1
reply
177
views
problem with ClusterRepro function
WGCNA
updated 8 weeks ago by
James W. MacDonald
65k • written 8 weeks ago by
Antonio.Aubry
• 0
0
votes
1
reply
305
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
553
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
1
vote
2
replies
692
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
318
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
1
reply
523
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
421
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
403
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
2.1k
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
506
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
630
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
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 28 days ago by
Ashley
• 0 • written 11 months ago by
zxc741xb
• 0
3
votes
6
replies
853
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
484
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
521
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
433
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
11 months ago
Levi
• 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
1
reply
895
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 10 weeks ago by
boczniak767
▴ 720 • written 15 months ago by
Kim
• 0
0
votes
2
replies
934
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 6 hours ago by
mariakenneth147
• 0 • written 17 months ago by
pharamac
• 0
0
votes
2
replies
1.3k
views
WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna
WGCNA
written 2.1 years ago by
bioinformaticssrm2011
• 0
0
votes
1
reply
1.1k
views
WGCNA Preservation error
preservation
WGCNA
updated 3 months ago by
Gail
• 0 • written 2.4 years ago by
Sara
• 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
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.1 years ago by
Colari19
▴ 60
0
votes
2
replies
823
views
Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA
Module Detection
updated 3 months ago by
dima11i
• 0 • written 4.6 years ago by
vsa1111
• 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
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
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 26 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
30 results • Page
1 of 1
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Replies
Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Guido Hooiveld
★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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