Showing : WGCNA • reset
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
16 hours ago • updated 15 hours ago Vinesh • 0
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32
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
2 days ago Reuben • 0
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1
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193
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 8 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
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4.0k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.8 years ago by ▴ 60
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153
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WGCNA module preservation using only adjacency matrix
WGCNA
9 weeks ago yang1641 • 0
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4
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577
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
3 months ago sukeshinik5 ▴ 20
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1
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414
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WGCNA
DEGselection RNASeqData WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
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243
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
4 months ago Fernanda • 0
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1
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331
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 4 months ago by ▴ 760 • written 4 months ago by • 0
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1
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346
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Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 4 months ago by 67k • written 4 months ago by • 0
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6
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2.8k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 21 months ago by • 0
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3
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3.6k
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WGNCA kME vs. kIM
WGCNA
updated 8 months ago by • 0 • written 9.3 years ago by ▴ 30
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284
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
8 months ago k200987 • 0
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2
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531
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
9 months ago Gimena • 0
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2
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586
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
9 months ago w.cookson • 0
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1
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449
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problem with ClusterRepro function
WGCNA
updated 10 months ago by 67k • written 10 months ago by • 0
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1
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883
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
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2
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1.2k
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 13 months ago by • 0
4
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3
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2.2k
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WGCNA documentation not available
WGCNA
written 13 months ago by ▴ 10
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2
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1.7k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 8 months ago by • 0 • written 2.2 years ago by • 0
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1
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1.3k
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WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 13 months ago by • 0 • written 3.1 years ago by • 0
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2
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1.3k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
13 months ago Levi • 0
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2
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549
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WGCNA less samples
RNA-Seq WGCNA Worms
14 months ago davca • 0
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1
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782
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 14 months ago by ★ 4.6k • written 14 months ago by • 0
1
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1
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738
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 15 months ago by ▴ 200 • written 15 months ago by ▴ 10
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1
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611
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 17 months ago by ★ 4.6k • written 17 months ago by • 0
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1
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4.6k
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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 18 months ago by 67k • written 18 months ago by • 0
1
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1
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721
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
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1
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1.0k
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 19 months ago by ★ 4.6k • written 19 months ago by ▴ 20
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5
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1.8k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 months ago by • 0 • written 19 months ago by • 0
3
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6
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1.2k
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 20 months ago by 52k • written 20 months ago by ▴ 10
1
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752
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 19 months ago by 43k • written 20 months ago by ▴ 20
2
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1
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846
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 20 months ago by ▴ 50 • written 20 months ago by ▴ 10
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601
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
20 months ago Levi • 0
3
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7
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1.8k
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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
20 months ago Ortega-C ▴ 10
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1
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710
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 20 months ago by ★ 4.6k • written 21 months ago by • 0
0
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0
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746
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
21 months ago Ortega-C ▴ 10
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2
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836
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WGCNA problem
WGCNA
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
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757
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
21 months ago Levi • 0
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0
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633
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Module Trait Corelation
WGCNA
22 months ago allanokwaro • 0
2
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3
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1.3k
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 22 months ago by ★ 4.6k • written 22 months ago by ▴ 20
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683
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How to draw module significance barplot?
module_significance barplot WGCNA
23 months ago Sooni ▴ 10
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690
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Multiple way network preservation
wgcna
23 months ago madzayasodara • 0
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762
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WGCNA TOM file empty
WGCNA TOM
23 months ago gianni.drm • 0
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1.2k
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
23 months ago gianni.drm • 0
0
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1
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1.3k
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WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 10 months ago by ▴ 740 • written 23 months ago by • 0
0
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1
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685
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In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 24 months ago by ▴ 50 • written 24 months ago by • 0
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825
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
2.0 years ago S • 0
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0
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809
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Problems running WGCNA
WGCNA
2.1 years ago S • 0
0
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0
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680
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coexpression networks
WGCNA igraph
2.1 years ago María José • 0
50 results • Page 1 of 1
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Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?
Answer: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounde…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by alserg ▴ 280
`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…
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Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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