Showing : wgcna • reset
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
1 day ago k200987 • 0
0
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2
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940
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 1 day ago by • 0 • written 17 months ago by • 0
11
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5
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7.4k
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Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 28 days ago by • 0 • written 9.1 years ago by ▴ 150
2
votes
5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 29 days ago by • 0 • written 11 months ago by • 0
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
0
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2
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205
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
0
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2
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238
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 weeks ago • updated 6 weeks ago w.cookson • 0
0
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1
reply
179
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problem with ClusterRepro function
WGCNA
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
0
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1
reply
896
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 10 weeks ago by ▴ 720 • written 15 months ago by • 0
0
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1
reply
311
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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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1
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1.1k
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WGCNA Preservation error
preservation WGCNA
updated 3 months ago by • 0 • written 2.4 years ago by • 0
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2
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824
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Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA Module Detection
updated 3 months ago by • 0 • written 4.6 years ago by • 0
1
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2
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697
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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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556
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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
5
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8
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3.9k
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Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
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2
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1.3k
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WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna WGCNA
written 2.1 years ago by • 0
4
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3
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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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1
reply
1.0k
views
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
0
votes
2
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319
views
WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
votes
1
reply
527
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
1
vote
1
reply
423
views
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
reply
405
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 8 months ago by ★ 4.1k • written 9 months ago by • 0
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1
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2.1k
views
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
6
votes
6
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2.7k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.1 years ago by ▴ 60
1
vote
1
reply
507
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
1
reply
635
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 11 months ago by ★ 4.1k • written 11 months ago by ▴ 20
1
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0
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488
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 42k • written 11 months ago by ▴ 20
3
votes
6
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858
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
2
votes
1
reply
522
views
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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436
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
1
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2
replies
2.7k
views
WGNCA kME vs. kIM
WGCNA
updated 12 months ago by • 0 • written 8.7 years ago by ▴ 30
3
votes
7
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1.2k
views
"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
reply
532
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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558
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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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617
views
WGCNA problem
WGCNA
updated 12 months ago by ▴ 10 • written 13 months ago by • 0
0
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0
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573
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
13 months ago Levi • 0
0
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4
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4.0k
views
WGCNA grey module
WGCNA
updated 13 months ago by ▴ 10 • written 6.0 years ago by ▴ 10
2
votes
3
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927
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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437
views
Module Trait Corelation
WGCNA
14 months ago allanokwaro • 0
0
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2
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2.0k
views
WGCNA adjust p value
WGCNA
written 2.8 years ago by ▴ 40
0
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0
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454
views
How to draw module significance barplot?
module_significance barplot WGCNA
15 months ago Sooni ▴ 10
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0
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489
views
Multiple way network preservation
wgcna
15 months ago madzayasodara • 0
0
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0
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543
views
WGCNA TOM file empty
WGCNA TOM
15 months ago gianni.drm • 0
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0
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845
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
15 months ago gianni.drm • 0
0
votes
1
reply
534
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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627
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
16 months ago S • 0
7
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9
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3.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 16 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
0
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4
replies
1.6k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation EPIC scale-free topology WGCNA
updated 16 months ago by • 0 • written 4.7 years ago by • 0
0
votes
1
reply
983
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 16 months ago by • 0 • written 2.5 years ago by ▴ 10
0
votes
0
replies
618
views
Problems running WGCNA
WGCNA
17 months ago S • 0
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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