Showing : wgcna • reset
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by • 0
0
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2
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195
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
5 weeks ago • updated 4 weeks ago Gimena • 0
0
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2
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231
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
5 weeks ago w.cookson • 0
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1
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171
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problem with ClusterRepro function
WGCNA
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
0
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1
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285
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 12 weeks ago by ★ 4.1k • written 12 weeks ago by • 0
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2
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534
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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
4
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3
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949
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WGCNA documentation not available
WGCNA
written 5 months ago by ▴ 10
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1
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904
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 5 months ago by • 0 • written 17 months ago by • 0
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1
reply
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
1
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2
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677
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 0
0
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2
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316
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
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1
reply
501
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
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1
reply
410
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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
0
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1
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396
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
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1
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2.0k
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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 9 months ago by 65k • written 9 months ago by • 0
1
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1
reply
497
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
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1
reply
613
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 10 months ago by ★ 4.1k • written 10 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 21 days ago by • 0 • written 10 months ago by • 0
3
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6
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844
views
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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0
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478
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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
reply
517
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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 11 months ago by ▴ 10
0
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0
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430
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 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 11 months ago by • 0 • written 8.6 years ago by ▴ 30
3
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7
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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
11 months ago Ortega-C ▴ 10
0
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1
reply
525
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
0
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0
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549
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
12 months ago Ortega-C ▴ 10
0
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2
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609
views
WGCNA problem
WGCNA
updated 12 months ago by ▴ 10 • written 12 months ago by • 0
0
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0
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568
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
13 months ago Levi • 0
0
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0
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426
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Module Trait Corelation
WGCNA
13 months ago allanokwaro • 0
2
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3
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898
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 14 months ago by ▴ 20
0
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0
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443
views
How to draw module significance barplot?
module_significance barplot WGCNA
14 months ago Sooni ▴ 10
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0
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486
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Multiple way network preservation
wgcna
14 months ago madzayasodara • 0
0
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0
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534
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WGCNA TOM file empty
WGCNA TOM
15 months ago gianni.drm • 0
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0
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827
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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
885
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WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 9 weeks ago by ▴ 720 • written 15 months ago by • 0
0
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1
reply
530
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
0
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0
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623
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago S • 0
0
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0
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605
views
Problems running WGCNA
WGCNA
16 months ago S • 0
0
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0
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528
views
coexpression networks
WGCNA igraph
17 months ago María José • 0
0
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0
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509
views
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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765
views
WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
17 months ago bioinformaticssrm2011 • 0
2
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1
reply
799
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 19 months ago by ▴ 50 • written 20 months ago by ▴ 10
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1
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829
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WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 20 months ago by ▴ 50 • written 20 months ago by ▴ 20
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0
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561
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MM-GS plot doesn't show any negative correlation
wgcna
21 months ago shubhankar.pawar • 0
0
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1
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962
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 22 months ago by • 0 • written 22 months ago by • 0
0
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0
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636
views
ARACNe Sample Size
grndata GRN ARACNE WGCNA
22 months ago Harrsha • 0
0
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0
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522
views
Enrichment in genomic regions
Enrichment clusterPro WGCNA
22 months ago María José • 0
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0
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613
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference SampledBlockWiseModules WGCNA
22 months ago as8020 • 0
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0
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425
views
WGCNA consensusMEDdissimilrity
WGCNA
24 months ago María José • 0
1
vote
3
replies
1.8k
views
WGCNA error
WGCNA
2.0 years ago ayabalbaa1990 • 0
50 results • Page 1 of 1
Recent ...
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Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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