Showing : wgcna • reset
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186
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
4 weeks ago Gimena • 0
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2
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228
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
5 weeks ago • updated 4 weeks ago w.cookson • 0
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1
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168
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problem with ClusterRepro function
WGCNA
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
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1
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269
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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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515
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by • 0
4
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3
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920
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WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
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2
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667
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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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312
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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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495
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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
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403
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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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1
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388
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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
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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
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495
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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
607
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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
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 16 days ago by • 0 • written 10 months ago by • 0
3
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6
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840
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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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0
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471
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 41k • written 11 months ago by ▴ 20
2
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1
reply
507
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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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428
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
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
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1
reply
522
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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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547
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
12 months ago Ortega-C ▴ 10
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2
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606
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WGCNA problem
WGCNA
updated 12 months ago by ▴ 10 • written 12 months ago by • 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 12 months ago by • 0
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0
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565
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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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421
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Module Trait Corelation
WGCNA
13 months ago allanokwaro • 0
2
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3
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892
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 20
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0
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440
views
How to draw module significance barplot?
module_significance barplot WGCNA
14 months ago Sooni ▴ 10
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485
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Multiple way network preservation
wgcna
14 months ago madzayasodara • 0
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531
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WGCNA TOM file empty
WGCNA TOM
14 months ago gianni.drm • 0
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0
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817
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
15 months ago gianni.drm • 0
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1
reply
879
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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
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528
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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0
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621
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago S • 0
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0
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601
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Problems running WGCNA
WGCNA
16 months ago S • 0
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0
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528
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coexpression networks
WGCNA igraph
17 months ago María José • 0
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0
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506
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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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1
reply
898
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 months ago by • 0 • written 17 months ago by • 0
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0
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758
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WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
17 months ago bioinformaticssrm2011 • 0
2
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1
reply
793
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 19 months ago by ▴ 50 • written 19 months ago by ▴ 10
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1
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824
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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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560
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MM-GS plot doesn't show any negative correlation
wgcna
21 months ago shubhankar.pawar • 0
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1
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960
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WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 21 months ago by • 0 • written 21 months ago by • 0
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0
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633
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ARACNe Sample Size
grndata GRN ARACNE WGCNA
22 months ago Harrsha • 0
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521
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Enrichment in genomic regions
Enrichment clusterPro WGCNA
22 months ago María José • 0
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0
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612
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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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420
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WGCNA consensusMEDdissimilrity
WGCNA
24 months ago María José • 0
1
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3
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1.8k
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WGCNA error
WGCNA
24 months ago ayabalbaa1990 • 0
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759
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
2.0 years ago chiwut.wong • 0
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0
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657
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FILTER GENES FOR WGCNA
WGCNA
2.0 years ago María José • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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