Showing : wgcna • reset
6
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3.7k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.6 years ago by ▴ 60
0
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0
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59
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WGCNA module preservation using only adjacency matrix
WGCNA
3 days ago yang1641 • 0
3
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4
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413
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
4 weeks ago sukeshinik5 ▴ 20
1
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1
reply
268
views
WGCNA
DEGselection RNASeqData WGCNA
updated 5 weeks ago by ▴ 760 • written 5 weeks ago by • 0
0
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0
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172
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
8 weeks ago Fernanda • 0
0
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1
reply
252
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 9 weeks ago by ▴ 760 • written 9 weeks ago by • 0
0
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1
reply
268
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Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 9 weeks ago by 67k • written 9 weeks ago by • 0
0
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6
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2.5k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 19 months ago by • 0
1
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3
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3.4k
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WGNCA kME vs. kIM
WGCNA
updated 5 months ago by • 0 • written 9.2 years ago by ▴ 30
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0
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241
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
6 months ago k200987 • 0
0
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2
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462
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
7 months ago Gimena • 0
0
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2
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531
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 months ago w.cookson • 0
0
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1
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379
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problem with ClusterRepro function
WGCNA
updated 8 months ago by 67k • written 8 months ago by • 0
0
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1
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738
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 9 months ago by ★ 4.5k • written 9 months ago by • 0
0
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2
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1.0k
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 11 months ago by • 0
4
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3
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1.9k
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WGCNA documentation not available
WGCNA
written 11 months ago by ▴ 10
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2
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1.5k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 6 months ago by • 0 • written 24 months ago by • 0
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1
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1.2k
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WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 11 months ago by • 0 • written 2.9 years ago by • 0
1
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2
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1.1k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
11 months ago • updated 10 months ago Levi • 0
0
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2
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516
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WGCNA less samples
RNA-Seq WGCNA Worms
12 months ago • updated 11 months ago davca • 0
0
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1
reply
731
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 12 months ago by ★ 4.5k • written 12 months ago by • 0
1
vote
1
reply
667
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 12 months ago by ▴ 200 • written 12 months ago by ▴ 10
0
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1
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572
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 15 months ago by ★ 4.5k • written 15 months ago by • 0
0
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1
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4.3k
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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 15 months ago by 67k • written 15 months ago by • 0
1
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1
reply
681
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 17 months ago by ★ 4.5k • written 17 months ago by • 0
0
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1
reply
923
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 17 months ago by ★ 4.5k • written 17 months ago by ▴ 20
2
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5
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1.7k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 7 months ago by • 0 • written 17 months ago by • 0
3
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6
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1.1k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 17 months ago by 51k • written 17 months ago by ▴ 10
1
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0
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705
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 17 months ago by 42k • written 18 months ago by ▴ 20
2
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1
reply
784
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 17 months ago by ▴ 50 • written 18 months ago by ▴ 10
0
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0
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565
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
18 months ago Levi • 0
3
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7
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1.7k
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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
18 months ago Ortega-C ▴ 10
0
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1
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666
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 18 months ago by ★ 4.5k • written 18 months ago by • 0
0
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0
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708
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
19 months ago • updated 18 months ago Ortega-C ▴ 10
0
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2
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796
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WGCNA problem
WGCNA
updated 19 months ago by ▴ 10 • written 19 months ago by • 0
0
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0
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717
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
19 months ago Levi • 0
0
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0
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585
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Module Trait Corelation
WGCNA
20 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 20 months ago by ★ 4.5k • written 20 months ago by ▴ 20
0
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0
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629
views
How to draw module significance barplot?
module_significance barplot WGCNA
21 months ago Sooni ▴ 10
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0
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653
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Multiple way network preservation
wgcna
21 months ago madzayasodara • 0
0
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0
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729
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WGCNA TOM file empty
WGCNA TOM
21 months ago gianni.drm • 0
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0
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1.1k
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
21 months ago gianni.drm • 0
0
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1
reply
1.2k
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WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 8 months ago by ▴ 740 • written 21 months ago by • 0
0
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1
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652
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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 21 months ago by ▴ 50 • written 21 months ago by • 0
0
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0
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773
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
22 months ago S • 0
0
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0
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768
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Problems running WGCNA
WGCNA
23 months ago S • 0
0
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0
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656
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coexpression networks
WGCNA igraph
23 months ago María José • 0
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0
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713
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
23 months ago Abdullah • 0
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
24 months ago • updated 7 weeks ago bioinformaticssrm2011 • 0
2
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1
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990
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WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 2.2 years ago by ▴ 50 • written 2.2 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: [How to construct a model.matrix ] by kyj2226 • 0
Thanks to you, I learn a lot. Many thanks, Yujin.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
thank you for your advice, I posted separate post.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Votes
Answer: [How to construct a model.matrix ]
C: DESeq2 baseMean values for each sample
C: DESeq2 baseMean values for each sample
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta
A: Some questions for remove batch effect by using mnnCorrect
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