Showing : wgcna • reset
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WGCNA - Outliers after creating sample tree
MicroarrayData WGCNA Microarray
4.7 years ago jpwl2 • 0
0
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1
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1.5k
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Differential Network analysis
WGCNA
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 10
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0
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1.5k
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WGCNA - TOM Similarity
WGCNA
4.7 years ago Svet • 0
0
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0
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1.2k
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
4.8 years ago wrzl • 0
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0
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1.7k
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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
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1
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2.1k
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installing GO.bd for WGCNA
GO.db WGCNA
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
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2
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3.3k
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DESeq2 counts as input for WGCNA
WGCNA DESeq2
4.9 years ago • updated 4.8 years ago Peny • 0
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1
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1.4k
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Correlation values from labeledHeatmap
WGCNA
updated 4.8 years ago by ▴ 100 • written 4.9 years ago by ▴ 40
15
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17
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30k
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WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 4.9 years ago by ▴ 760 • written 9.1 years ago by ▴ 40
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0
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867
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Do p-values of Gene Significance per gene need to be FDR corrected?
WGCNA
4.9 years ago Miguel.Cosenza ▴ 10
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2
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2.1k
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Use of RSEM counts in WGCNA
rsemmed RSEM WGCNA
4.9 years ago harelarik ▴ 60
1
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1
reply
846
views
Any possiblity applying
WGCNA
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 40
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0
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1.7k
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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
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7
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4.8k
views
WGCNA: Topological Overlap Matrix (TOM) Values Greater Than 1
WGCNA
5.1 years ago • updated 5.0 years ago teresisc ▴ 10
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3
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1.3k
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WGCNA soft threshold slope
wgcna
written 5.1 years ago by • 0
0
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2
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1.2k
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WGCNA unpaired quantitative traits
wgcna
5.2 years ago lidia.mateo ▴ 30
0
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2
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3.2k
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Soft-threshold in WGCNA
wgcna network bicor threshold
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 80
0
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9
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4.7k
views
WGCNA module trait relationship issue
wgcna
updated 5.3 years ago by ★ 3.0k • written 5.3 years ago by • 0
4
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2
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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 68k • written 5.5 years ago by • 0
5
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8
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6.0k
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WGCNA tutorial II
WGCNA female and male datasets
updated 3.6 years ago by • 0 • written 5.5 years ago by ▴ 60
3
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5
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1.9k
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Samples replications in WGCNA?
WGCNA
updated 5.5 years ago by ★ 4.0k • written 5.5 years ago by ▴ 60
2
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4
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1.5k
views
Error in "Relating the consensus modules to female set-specific modules"
WGCNA
updated 3.4 years ago by ▴ 10 • written 5.5 years ago by ▴ 60
1
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1
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3.4k
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Calculating TOM in blockwise WGCNA
WGCNA TOM block-wise
updated 5.6 years ago by ★ 3.0k • written 5.6 years ago by ▴ 10
0
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2
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1.3k
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Generalised TOM over TOM for wgcna
WGCNA TOM
updated 5.6 years ago by ★ 3.0k • written 5.6 years ago by • 0
1
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5
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2.8k
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Need comments/advices for WGCNA network visualization
WGCNA
5.6 years ago minyaaa9058 ▴ 40
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8
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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 ★ 3.0k • written 5.6 years ago by • 0
0
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0
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1.2k
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WGCNA for Dose-Response RNA-Seq Data
wgcna network analysis
5.6 years ago jwilliamblamer • 0
0
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2
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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
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1
reply
1.1k
views
WGCNA sample number reduction
wgcna networkanalysis
updated 5.7 years ago by 4.2k • written 5.7 years ago by ▴ 10
5
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2
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6.8k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 30
11
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2
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6.4k
views
Filtering low variance genes for WGCNA
deseq2 WGCNA
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 40
1
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0
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1.4k
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WGCNA trait order in heat map
wgcna WGCNA wgcna package
5.8 years ago coyoung ▴ 10
3
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3
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4.1k
views
WGCNA module colors not displaying correctly
WGCNA
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 40
0
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2
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12k
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Unable to install, update WGCNA and GO.db
WGCNA software error
5.8 years ago rproendo ▴ 30
2
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3
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2.9k
views
Interpretaion of dendrogram height in WGCNA?
WGCNA coexpression network
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 30
0
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0
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916
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How to label module colors in WGCNA TOMplot
WGCNA TOMplot module-colors
5.8 years ago saadmurtazakhan ▴ 10
0
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6
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2.2k
views
Overlapping genes between gene modules in WGCNA
WGCNA
5.8 years ago shresthavivek18 • 0
2
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4
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2.7k
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Case-control study using WGCNA
wgcna network rna-seq
5.9 years ago Arindam ▴ 80
2
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4
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4.0k
views
WGCNA parallelization multi thread for blockwiseModules and TOMsimilarity
wgcna parallelization
updated 12 months ago by ★ 3.0k • written 5.9 years ago by ▴ 10
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2
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2.3k
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WGCNA module Eigengene PC1 and expression correlation
WGCNA DESeq2 RNA-Seq
5.9 years ago Sri Dewi • 0
1
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4
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3.0k
views
Removal of batch effects from RNA-seq data for WGCNA
limma deseq2 wgcna RUVseq
5.9 years ago Arindam ▴ 80
3
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6
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6.4k
views
WGCNA gene significance and module membership
WGCNA R
updated 3.0 years ago by ★ 3.0k • written 6.0 years ago by • 0
0
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1
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1.2k
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plotEigengeneNetworks WGCNA add ME labels to left side of figure
R WGCNA
6.0 years ago normingt • 0
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6
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2.6k
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Breaking down the output from plotEigengeneNetworks()
WGCNA Heatmap EigenGeneNetworks
6.0 years ago l.s.wijaya • 0
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2
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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 • 0 • written 6.0 years ago by • 0
8
votes
6
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6.9k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by ▴ 180
2
votes
4
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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 ★ 3.0k • written 6.1 years ago by • 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 ▴ 10 • written 6.1 years ago by ▴ 40
1
vote
1
reply
2.4k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
0
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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 • 0 • written 6.2 years ago by • 0
335 results • Page 3 of 7
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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…
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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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