Showing : wgcna • reset
11
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5
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7.4k
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Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 15 days ago by • 0 • written 9.1 years ago by ▴ 150
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 16 days ago by • 0 • written 10 months ago by • 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
0
votes
2
replies
186
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 weeks ago Gimena • 0
0
votes
2
replies
228
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
5 weeks ago • updated 4 weeks ago w.cookson • 0
0
votes
1
reply
169
views
problem with ClusterRepro function
WGCNA
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
0
votes
1
reply
879
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 9 weeks ago by ▴ 720 • written 15 months ago by • 0
0
votes
1
reply
269
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 12 weeks ago by ★ 4.1k • written 12 weeks ago by • 0
0
votes
1
reply
1.1k
views
WGCNA Preservation error
preservation WGCNA
updated 3 months ago by • 0 • written 2.3 years ago by • 0
0
votes
2
replies
806
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 • 0 • written 4.5 years ago by • 0
1
vote
2
replies
667
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
518
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by • 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 ▴ 40
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 • 0
4
votes
3
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920
views
WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
0
votes
1
reply
900
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
997
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 5 months ago by • 0 • written 2.4 years ago by • 0
0
votes
2
replies
312
views
WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
votes
1
reply
496
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
vote
1
reply
403
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by ▴ 190 • written 6 months ago by ▴ 10
0
votes
1
reply
389
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
1
reply
2.0k
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 65k • written 9 months ago by • 0
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
1
vote
1
reply
496
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
1
reply
607
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 20
1
vote
0
replies
472
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 41k • written 11 months ago by ▴ 20
3
votes
6
replies
841
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
2
votes
1
reply
507
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 11 months ago by ▴ 50 • written 11 months ago by ▴ 10
0
votes
0
replies
428
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
1
vote
2
replies
2.7k
views
WGNCA kME vs. kIM
WGCNA
updated 11 months ago by • 0 • written 8.6 years ago by ▴ 30
3
votes
7
replies
1.2k
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
11 months ago Ortega-C ▴ 10
0
votes
1
reply
522
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
0
replies
547
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
12 months ago Ortega-C ▴ 10
0
votes
2
replies
606
views
WGCNA problem
WGCNA
updated 12 months ago by ▴ 10 • written 12 months ago by • 0
0
votes
0
replies
566
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
13 months ago Levi • 0
0
votes
4
replies
3.9k
views
WGCNA grey module
WGCNA
updated 13 months ago by ▴ 10 • written 6.0 years ago by ▴ 10
2
votes
3
replies
892
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 20
0
votes
0
replies
421
views
Module Trait Corelation
WGCNA
13 months ago allanokwaro • 0
0
votes
2
replies
1.9k
views
WGCNA adjust p value
WGCNA
written 2.8 years ago by ▴ 40
0
votes
0
replies
441
views
How to draw module significance barplot?
module_significance barplot WGCNA
14 months ago Sooni ▴ 10
0
votes
0
replies
485
views
Multiple way network preservation
wgcna
14 months ago madzayasodara • 0
0
votes
0
replies
532
views
WGCNA TOM file empty
WGCNA TOM
15 months ago gianni.drm • 0
0
votes
0
replies
818
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
15 months ago gianni.drm • 0
0
votes
1
reply
528
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 15 months ago by ▴ 50 • written 15 months ago by • 0
0
votes
0
replies
622
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago S • 0
7
votes
9
replies
3.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 15 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
0
votes
4
replies
1.6k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 15 months ago by • 0 • written 4.7 years ago by • 0
0
votes
1
reply
974
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 15 months ago by • 0 • written 2.4 years ago by ▴ 10
0
votes
0
replies
601
views
Problems running WGCNA
WGCNA
16 months ago S • 0
0
votes
0
replies
528
views
coexpression networks
WGCNA igraph
17 months ago María José • 0
50 results • Page 1 of 1
Recent ...
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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