Showing : WGCNA • reset
1
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312
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 3 months ago by ▴ 10
0
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4
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634
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Issue with Soft-Thresholding in WGCNA
WGCNA
written 7 months ago by • 0
3
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4
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8.0k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.3 years ago by ▴ 80
0
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5
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856
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WGCNA
WGCNA Normalization RNASeq
written 8 months ago by • 0
6
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8
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5.6k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.6 years ago by ▴ 60
0
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2
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5.2k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 4 months ago by • 0 • written 2.6 years ago by • 0
0
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1
reply
889
views
WGCNA
WGCNA DESeq2
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
11
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6
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4.7k
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WGCNA with paired samples
wgcna paired samples exercise
updated 8 months ago by • 0 • written 9.2 years ago by ▴ 60
0
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1
reply
743
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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1
reply
544
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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2
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522
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
9 months ago Vinesh • 0
0
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1
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330
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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1
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672
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
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0
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435
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WGCNA module preservation using only adjacency matrix
WGCNA
12 months ago yang1641 • 0
3
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4
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1.5k
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
13 months ago sukeshinik5 ▴ 20
1
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1
reply
949
views
WGCNA
DEGselection RNASeqData WGCNA
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
0
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0
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591
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
13 months ago Fernanda • 0
0
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1
reply
619
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
0
votes
1
reply
646
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 14 months ago by 68k • written 14 months ago by • 0
1
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3
replies
4.4k
views
WGNCA kME vs. kIM
WGCNA
updated 18 months ago by • 0 • written 10.2 years ago by ▴ 30
0
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0
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517
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
18 months ago k200987 • 0
0
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2
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860
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
19 months ago Gimena • 0
0
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2
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948
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
19 months ago w.cookson • 0
0
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1
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685
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problem with ClusterRepro function
WGCNA
updated 20 months ago by 68k • written 20 months ago by • 0
0
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1
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1.3k
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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2
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1.7k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 23 months ago by • 0
4
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3
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3.0k
views
WGCNA documentation not available
WGCNA
written 23 months ago by ▴ 10
0
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2
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2.5k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 18 months ago by • 0 • written 3.0 years ago by • 0
0
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1
reply
1.6k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 23 months ago by • 0 • written 3.9 years ago by • 0
1
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2
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1.8k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
23 months ago • updated 22 months ago Levi • 0
0
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2
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790
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WGCNA less samples
RNA-Seq WGCNA Worms
24 months ago davca • 0
0
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1
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1.0k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
1
vote
2
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1.3k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.1 years ago by ▴ 10
0
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1
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832
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
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5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
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1
reply
941
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
1.4k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 20
2
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5
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2.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 months ago by • 0 • written 2.4 years ago by • 0
3
votes
6
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1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
1
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0
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1.0k
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 20
2
votes
1
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1.1k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 2.5 years ago by ▴ 50 • written 2.5 years ago by ▴ 10
0
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0
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802
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.5 years ago Levi • 0
3
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7
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2.5k
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
2.5 years ago Ortega-C ▴ 10
0
votes
1
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892
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
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0
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961
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
2.6 years ago Ortega-C ▴ 10
0
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2
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1.1k
views
WGCNA problem
WGCNA
updated 2.6 years ago by ▴ 10 • written 2.6 years ago by • 0
0
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0
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958
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.6 years ago Levi • 0
0
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0
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798
views
Module Trait Corelation
WGCNA
2.6 years ago allanokwaro • 0
2
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3
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1.8k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.6 years ago by ★ 5.0k • written 2.7 years ago by ▴ 20
0
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0
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892
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How to draw module significance barplot?
module_significance barplot WGCNA
2.7 years ago Sooni ▴ 10
335 results • Page 1 of 7
Recent ...
Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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Scholar to James W. MacDonald 68k
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