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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
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6
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4.0k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.7 years ago by ▴ 60
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134
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WGCNA module preservation using only adjacency matrix
WGCNA
7 weeks ago yang1641 • 0
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4
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524
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
11 weeks ago sukeshinik5 ▴ 20
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373
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WGCNA
DEGselection RNASeqData WGCNA
updated 12 weeks ago by ▴ 760 • written 12 weeks ago by • 0
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226
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
3 months ago Fernanda • 0
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1
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314
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
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326
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Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 3 months ago by 67k • written 3 months ago by • 0
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2.7k
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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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3.5k
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WGNCA kME vs. kIM
WGCNA
updated 7 months ago by • 0 • written 9.3 years ago by ▴ 30
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274
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
7 months ago k200987 • 0
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513
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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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572
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
9 months ago w.cookson • 0
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440
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problem with ClusterRepro function
WGCNA
updated 9 months ago by 67k • written 9 months ago by • 0
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844
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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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1.1k
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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
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2.1k
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WGCNA documentation not available
WGCNA
written 13 months ago by ▴ 10
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1.6k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 7 months ago by • 0 • written 2.1 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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1.2k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
13 months ago • updated 12 months ago Levi • 0
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2
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541
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WGCNA less samples
RNA-Seq WGCNA Worms
13 months ago davca • 0
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1
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771
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
1
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1
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723
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 14 months ago by ▴ 200 • written 14 months ago by ▴ 10
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599
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TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
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1
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4.5k
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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 17 months ago by 67k • written 17 months ago by • 0
1
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1
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708
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
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1
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988
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 18 months ago by ★ 4.6k • written 18 months ago by ▴ 20
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5
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1.7k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 months ago by • 0 • written 18 months ago by • 0
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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 19 months ago by 52k • written 19 months ago by ▴ 10
1
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745
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 19 months ago by 43k • written 19 months ago by ▴ 20
2
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1
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833
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 19 months ago by ▴ 50 • written 19 months ago by ▴ 10
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595
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
19 months ago Levi • 0
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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
19 months ago Ortega-C ▴ 10
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704
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 20 months ago by ★ 4.6k • written 20 months ago by • 0
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736
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
20 months ago Ortega-C ▴ 10
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2
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828
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WGCNA problem
WGCNA
updated 20 months ago by ▴ 10 • written 20 months ago by • 0
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748
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
21 months ago Levi • 0
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623
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Module Trait Corelation
WGCNA
21 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 21 months ago by ★ 4.6k • written 22 months ago by ▴ 20
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672
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How to draw module significance barplot?
module_significance barplot WGCNA
22 months ago Sooni ▴ 10
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679
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Multiple way network preservation
wgcna
22 months ago madzayasodara • 0
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755
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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
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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
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1
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677
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 23 months ago by ▴ 50 • written 23 months ago by • 0
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813
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
23 months ago S • 0
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801
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Problems running WGCNA
WGCNA
2.0 years ago S • 0
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676
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coexpression networks
WGCNA igraph
2.1 years ago María José • 0
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733
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
2.1 years ago Abdullah • 0
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0
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1.1k
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WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.1 years ago • updated 3 months ago bioinformaticssrm2011 • 0
50 results • Page 1 of 1
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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…
Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k
I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…
Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k
I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find: ```` # estimate d…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Votes
C: How does edgeR cpm function calculate log(CPM) values?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
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