Showing : WGCNA • reset
3
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.1 years ago by ▴ 80
1
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1
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138
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 4 weeks ago by 53k • written 4 weeks ago by ▴ 10
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5
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694
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WGCNA
WGCNA Normalization RNASeq
written 6 months ago by • 0
6
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8
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5.4k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.4 years ago by ▴ 60
0
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2
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5.0k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 8 weeks ago by • 0 • written 2.4 years ago by • 0
0
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1
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834
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WGCNA
WGCNA DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
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2
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464
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Issue with Soft-Thresholding in WGCNA
WGCNA
updated 8 weeks ago by • 0 • written 5 months ago by • 0
11
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6
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4.6k
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WGCNA with paired samples
wgcna paired samples exercise
updated 6 months ago by • 0 • written 9.1 years ago by ▴ 60
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1
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689
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
0
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1
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410
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
0
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2
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433
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
7 months ago Vinesh • 0
0
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1
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270
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Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
0
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1
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553
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 9 months ago by ★ 4.9k • written 9 months ago by • 0
0
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0
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374
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WGCNA module preservation using only adjacency matrix
WGCNA
10 months ago yang1641 • 0
3
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4
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1.4k
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
11 months ago sukeshinik5 ▴ 20
1
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1
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802
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WGCNA
DEGselection RNASeqData WGCNA
updated 11 months ago by ▴ 760 • written 11 months ago by • 0
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0
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547
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
11 months ago Fernanda • 0
0
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1
reply
578
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 12 months ago by ▴ 760 • written 12 months ago by • 0
0
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1
reply
606
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Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
3
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4.3k
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WGNCA kME vs. kIM
WGCNA
updated 15 months ago by • 0 • written 10.0 years ago by ▴ 30
0
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0
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466
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
16 months ago k200987 • 0
0
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2
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793
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
17 months ago Gimena • 0
0
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2
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879
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
17 months ago w.cookson • 0
0
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1
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641
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problem with ClusterRepro function
WGCNA
updated 18 months ago by 68k • written 18 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 19 months ago by ★ 4.9k • written 19 months ago by • 0
0
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2
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1.6k
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 21 months ago by • 0
4
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3
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2.9k
views
WGCNA documentation not available
WGCNA
written 21 months ago by ▴ 10
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2
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2.4k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 16 months ago by • 0 • written 2.8 years ago by • 0
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1
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1.5k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 21 months ago by • 0 • written 3.8 years ago by • 0
1
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2
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1.7k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
21 months ago • updated 20 months ago Levi • 0
0
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2
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731
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WGCNA less samples
RNA-Seq WGCNA Worms
22 months ago • updated 21 months ago davca • 0
0
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1
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977
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 22 months ago by ★ 4.9k • written 22 months ago by • 0
1
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2
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1.2k
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 22 months ago by ▴ 10
0
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1
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788
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TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.1 years ago by ★ 4.9k • written 2.1 years ago by • 0
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1
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5.0k
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Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
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1
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880
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by • 0
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1
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1.3k
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by ▴ 20
2
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5
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2.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 17 months ago by • 0 • written 2.3 years ago by • 0
3
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6
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1.5k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
1
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0
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966
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 20
2
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1
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1.1k
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 2.3 years ago by ▴ 50 • written 2.3 years ago by ▴ 10
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0
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767
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.3 years ago Levi • 0
3
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7
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2.3k
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"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
2.3 years ago Ortega-C ▴ 10
0
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1
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843
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.4 years ago by ★ 4.9k • written 2.4 years ago by • 0
0
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0
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919
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
2.4 years ago Ortega-C ▴ 10
0
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2
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1.0k
views
WGCNA problem
WGCNA
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by • 0
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0
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914
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.4 years ago Levi • 0
0
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0
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762
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Module Trait Corelation
WGCNA
2.5 years ago allanokwaro • 0
2
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3
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1.7k
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by ▴ 20
0
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0
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848
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How to draw module significance barplot?
module_significance barplot WGCNA
2.6 years ago Sooni ▴ 10
335 results • Page 1 of 7
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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