Showing : wgcna • reset
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
4 days ago k200987 • 0
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5
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1.7k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by • 0
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2
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207
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
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2
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243
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 weeks ago • updated 6 weeks ago w.cookson • 0
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1
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184
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problem with ClusterRepro function
WGCNA
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
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1
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318
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
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561
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 5 months ago by • 0
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1.0k
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WGCNA documentation not available
WGCNA
written 5 months ago by ▴ 10
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951
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 days ago by • 0 • written 18 months ago by • 0
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1
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1.0k
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WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 5 months ago by • 0 • written 2.4 years ago by • 0
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2
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700
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 0
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2
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325
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
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1
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529
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
1
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1
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425
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by ▴ 190 • written 6 months ago by ▴ 10
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408
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TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
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1
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2.1k
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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 9 months ago by 65k • written 9 months ago by • 0
1
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1
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509
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
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1
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643
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 11 months ago by ★ 4.1k • written 11 months ago by ▴ 20
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 4 weeks ago by • 0 • written 11 months ago by • 0
3
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6
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862
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
1
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492
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 42k • written 11 months ago by ▴ 20
2
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1
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528
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 11 months ago by ▴ 50 • written 12 months ago by ▴ 10
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440
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
12 months ago Levi • 0
1
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2
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2.7k
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WGNCA kME vs. kIM
WGCNA
updated 12 months ago by • 0 • written 8.7 years ago by ▴ 30
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1.2k
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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
12 months ago Ortega-C ▴ 10
0
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1
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534
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
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0
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562
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
13 months ago • updated 12 months ago Ortega-C ▴ 10
0
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2
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620
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WGCNA problem
WGCNA
updated 13 months ago by ▴ 10 • written 13 months ago by • 0
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577
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
13 months ago Levi • 0
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0
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442
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Module Trait Corelation
WGCNA
14 months ago allanokwaro • 0
2
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3
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931
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by ▴ 20
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457
views
How to draw module significance barplot?
module_significance barplot WGCNA
15 months ago Sooni ▴ 10
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493
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Multiple way network preservation
wgcna
15 months ago madzayasodara • 0
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544
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WGCNA TOM file empty
WGCNA TOM
15 months ago gianni.drm • 0
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851
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
15 months ago gianni.drm • 0
0
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1
reply
901
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 11 weeks ago by ▴ 720 • written 15 months ago by • 0
0
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1
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538
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 15 months ago by ▴ 50 • written 15 months ago by • 0
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632
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
16 months ago S • 0
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0
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623
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Problems running WGCNA
WGCNA
17 months ago S • 0
0
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539
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coexpression networks
WGCNA igraph
17 months ago María José • 0
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0
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527
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
17 months ago Abdullah • 0
0
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0
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790
views
WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
18 months ago bioinformaticssrm2011 • 0
2
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1
reply
813
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WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 20 months ago by ▴ 50 • written 20 months ago by ▴ 10
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1
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837
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WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 20 months ago by ▴ 50 • written 21 months ago by ▴ 20
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0
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570
views
MM-GS plot doesn't show any negative correlation
wgcna
22 months ago shubhankar.pawar • 0
0
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1
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976
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 22 months ago by • 0 • written 22 months ago by • 0
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0
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642
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ARACNe Sample Size
grndata GRN ARACNE WGCNA
22 months ago Harrsha • 0
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0
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527
views
Enrichment in genomic regions
Enrichment clusterPro WGCNA
22 months ago María José • 0
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0
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620
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How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference SampledBlockWiseModules WGCNA
22 months ago as8020 • 0
0
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0
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429
views
WGCNA consensusMEDdissimilrity
WGCNA
2.0 years ago María José • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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