Showing : wgcna • reset
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
2 days ago k200987 • 0
0
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2
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946
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 2 days 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 29 days ago by • 0 • written 9.2 years ago by ▴ 150
2
votes
5
replies
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
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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
0
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2
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241
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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
183
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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
reply
900
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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
reply
317
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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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825
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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 4 months ago by • 0 • written 4.6 years ago by • 0
1
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2
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699
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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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558
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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
views
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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votes
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
0
votes
2
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324
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
votes
1
reply
528
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
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
0
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1
reply
406
views
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
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
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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
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1
reply
508
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
641
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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490
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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860
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
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1
reply
525
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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439
views
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
views
WGNCA kME vs. kIM
WGCNA
updated 12 months ago by • 0 • written 8.7 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
12 months ago Ortega-C ▴ 10
0
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1
reply
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
0
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0
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560
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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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619
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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576
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
13 months ago Levi • 0
0
votes
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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930
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.1k • written 14 months ago by ▴ 20
0
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0
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439
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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456
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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491
views
Multiple way network preservation
wgcna
15 months ago madzayasodara • 0
0
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0
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543
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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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849
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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
537
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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630
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
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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
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621
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Problems running WGCNA
WGCNA
17 months ago S • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
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
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