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wgcna
•
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0
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2
replies
2.3k
views
WGCNA - Outliers after creating sample tree
MicroarrayData
WGCNA
Microarray
4.7 years ago
jpwl2
• 0
0
votes
1
reply
1.5k
views
Differential Network analysis
WGCNA
updated 4.7 years ago by
Kevin Blighe
★ 4.0k • written 4.7 years ago by
Hanna
▴ 10
0
votes
0
replies
1.5k
views
WGCNA - TOM Similarity
WGCNA
4.7 years ago
Svet
• 0
0
votes
0
replies
1.2k
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq
DESeq2
WGCNA
Normalization
4.8 years ago
wrzl
• 0
0
votes
0
replies
1.7k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network
StatisticalMethod
WGCNA
ExpressionData
4.8 years ago
jol.espinoz
▴ 40
1
vote
1
reply
2.1k
views
installing GO.bd for WGCNA
GO.db
WGCNA
updated 4.9 years ago by
James W. MacDonald
68k • written 4.9 years ago by
VictoriaL
• 0
1
vote
2
replies
3.3k
views
DESeq2 counts as input for WGCNA
WGCNA
DESeq2
4.9 years ago • updated 4.8 years ago
Peny
• 0
0
votes
1
reply
1.4k
views
Correlation values from labeledHeatmap
WGCNA
updated 4.8 years ago by
nick.eagles
▴ 100 • written 4.9 years ago by
R
▴ 40
15
votes
17
replies
30k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 4.9 years ago by
Lluís Revilla Sancho
▴ 760 • written 9.1 years ago by
jol.espinoz
▴ 40
0
votes
0
replies
867
views
Do p-values of Gene Significance per gene need to be FDR corrected?
WGCNA
4.9 years ago
Miguel.Cosenza
▴ 10
0
votes
2
replies
2.1k
views
Use of RSEM counts in WGCNA
rsemmed
RSEM
WGCNA
4.9 years ago
harelarik
▴ 60
1
vote
1
reply
846
views
Any possiblity applying
WGCNA
updated 5.0 years ago by
Kevin Blighe
★ 4.0k • written 5.0 years ago by
adR
▴ 40
0
votes
0
replies
1.7k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule
microarray
RNA-seq
WGCNA
5.0 years ago
modarzi
▴ 10
2
votes
7
replies
4.8k
views
WGCNA: Topological Overlap Matrix (TOM) Values Greater Than 1
WGCNA
5.1 years ago • updated 5.0 years ago
teresisc
▴ 10
0
votes
3
replies
1.3k
views
WGCNA soft threshold slope
wgcna
written 5.1 years ago by
kiddos17
• 0
0
votes
2
replies
1.2k
views
WGCNA unpaired quantitative traits
wgcna
5.2 years ago
lidia.mateo
▴ 30
0
votes
2
replies
3.2k
views
Soft-threshold in WGCNA
wgcna
network
bicor
threshold
updated 5.2 years ago by
Peter Langfelder
★ 3.0k • written 5.2 years ago by
Arindam
▴ 80
0
votes
9
replies
4.7k
views
WGCNA module trait relationship issue
wgcna
updated 5.3 years ago by
Peter Langfelder
★ 3.0k • written 5.3 years ago by
zen
• 0
4
votes
2
replies
2.3k
views
The Mac version of R always reports an error when installing WGCNA
software error
WGCNA
mac
updated 5.5 years ago by
James W. MacDonald
68k • written 5.5 years ago by
562125035
• 0
5
votes
8
replies
6.0k
views
WGCNA tutorial II
WGCNA
female and male datasets
updated 3.6 years ago by
synat.keam
• 0 • written 5.5 years ago by
bahmanik@msu.edu
▴ 60
3
votes
5
replies
1.9k
views
Samples replications in WGCNA?
WGCNA
updated 5.5 years ago by
Kevin Blighe
★ 4.0k • written 5.5 years ago by
bahmanik@msu.edu
▴ 60
2
votes
4
replies
1.5k
views
Error in "Relating the consensus modules to female set-specific modules"
WGCNA
updated 3.4 years ago by
annamariabugaj
▴ 10 • written 5.5 years ago by
bahmanik@msu.edu
▴ 60
1
vote
1
reply
3.4k
views
Calculating TOM in blockwise WGCNA
WGCNA
TOM
block-wise
updated 5.6 years ago by
Peter Langfelder
★ 3.0k • written 5.6 years ago by
C A
▴ 10
0
votes
2
replies
1.3k
views
Generalised TOM over TOM for wgcna
WGCNA
TOM
updated 5.6 years ago by
Peter Langfelder
★ 3.0k • written 5.6 years ago by
n.naharfancy
• 0
1
vote
5
replies
2.8k
views
Need comments/advices for WGCNA network visualization
WGCNA
5.6 years ago
minyaaa9058
▴ 40
0
votes
8
replies
5.3k
views
WGCNA Soft Thresholding: Why does my y-axis for signed R^2 (R-squared) go above 1 and asymptote at 1.5?
WGCNA
Soft Thresholding
updated 5.6 years ago by
Peter Langfelder
★ 3.0k • written 5.6 years ago by
DWF
• 0
0
votes
0
replies
1.2k
views
WGCNA for Dose-Response RNA-Seq Data
wgcna
network analysis
5.6 years ago
jwilliamblamer
• 0
0
votes
2
replies
1.5k
views
Study Modules significance (or Modules Preservation) in ONE network
modulePreservation
WGCNA
modules significance
permutation
7.6 years ago • updated 5.6 years ago
harelarik
▴ 60
1
vote
1
reply
1.1k
views
WGCNA sample number reduction
wgcna
networkanalysis
updated 5.7 years ago by
shepherl
4.2k • written 5.7 years ago by
anjanaram1
▴ 10
5
votes
2
replies
6.8k
views
[WGCNA]How to visualize network of genes in one module
WGCNA
network
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
huynguyen96.dnu
▴ 30
11
votes
2
replies
6.4k
views
Filtering low variance genes for WGCNA
deseq2
WGCNA
updated 5.8 years ago by
Peter Langfelder
★ 3.0k • written 5.8 years ago by
minyaaa9058
▴ 40
1
vote
0
replies
1.4k
views
WGCNA trait order in heat map
wgcna
WGCNA
wgcna package
5.8 years ago
coyoung
▴ 10
3
votes
3
replies
4.1k
views
WGCNA module colors not displaying correctly
WGCNA
updated 5.8 years ago by
Peter Langfelder
★ 3.0k • written 5.8 years ago by
minyaaa9058
▴ 40
0
votes
2
replies
12k
views
Unable to install, update WGCNA and GO.db
WGCNA
software error
5.8 years ago
rproendo
▴ 30
2
votes
3
replies
2.9k
views
Interpretaion of dendrogram height in WGCNA?
WGCNA
coexpression network
updated 5.8 years ago by
Peter Langfelder
★ 3.0k • written 5.8 years ago by
huynguyen96.dnu
▴ 30
0
votes
0
replies
916
views
How to label module colors in WGCNA TOMplot
WGCNA
TOMplot
module-colors
5.8 years ago
saadmurtazakhan
▴ 10
0
votes
6
replies
2.2k
views
Overlapping genes between gene modules in WGCNA
WGCNA
5.8 years ago
shresthavivek18
• 0
2
votes
4
replies
2.7k
views
Case-control study using WGCNA
wgcna
network
rna-seq
5.9 years ago
Arindam
▴ 80
2
votes
4
replies
4.0k
views
WGCNA parallelization multi thread for blockwiseModules and TOMsimilarity
wgcna
parallelization
updated 12 months ago by
Peter Langfelder
★ 3.0k • written 5.9 years ago by
bioming
▴ 10
0
votes
2
replies
2.3k
views
WGCNA module Eigengene PC1 and expression correlation
WGCNA
DESeq2
RNA-Seq
5.9 years ago
Sri Dewi
• 0
1
vote
4
replies
3.0k
views
Removal of batch effects from RNA-seq data for WGCNA
limma
deseq2
wgcna
RUVseq
5.9 years ago
Arindam
▴ 80
3
votes
6
replies
6.4k
views
WGCNA gene significance and module membership
WGCNA
R
updated 3.0 years ago by
Peter Langfelder
★ 3.0k • written 6.0 years ago by
VictoriaL
• 0
0
votes
1
reply
1.2k
views
plotEigengeneNetworks WGCNA add ME labels to left side of figure
R
WGCNA
6.0 years ago
normingt
• 0
0
votes
6
replies
2.6k
views
Breaking down the output from plotEigengeneNetworks()
WGCNA
Heatmap
EigenGeneNetworks
6.0 years ago
l.s.wijaya
• 0
0
votes
2
replies
1.4k
views
Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA
Module Detection
updated 21 months ago by
dima11i
• 0 • written 6.0 years ago by
vsa1111
• 0
8
votes
6
replies
6.9k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 6.1 years ago by
Peter Langfelder
★ 3.0k • written 6.1 years ago by
charles.foster
▴ 180
2
votes
4
replies
9.2k
views
WGCNA: 1) low soft thresholding power, 2) large modules, 3) best correlation for different types of trait variables
WGCNA
updated 6.1 years ago by
Peter Langfelder
★ 3.0k • written 6.1 years ago by
stu111538
• 0
1
vote
12
replies
7.9k
views
WGCNA: correlations module-traits, and module membership-gene significance
WGCNA
co-expression analysis
gene significance
module membership
module-trait relationship
updated 3.4 years ago by
annamariabugaj
▴ 10 • written 6.1 years ago by
rodrigo.duarte88
▴ 40
1
vote
1
reply
2.4k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 6.1 years ago by
Gordon Smyth
53k • written 6.1 years ago by
bioming
▴ 10
0
votes
4
replies
2.5k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 2.8 years ago by
shuo
• 0 • written 6.2 years ago by
enora.fremy
• 0
335 results • Page
3 of 7
Recent ...
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Answer: Using DESeq2 for age prediction
by
ATpoint
★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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