Showing : wgcna • reset
8
votes
17
replies
14k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA Sample Size Outliers
updated 8.7 years ago by • 0 • written 9.2 years ago by ▴ 150
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.4 years ago by ▴ 730 • written 7.6 years ago by ▴ 40
1
vote
12
replies
4.6k
views
WGCNA: correlations module-traits, and module membership-gene significance
WGCNA co-expression analysis gene significance module membership module-trait relationship
updated 23 months ago by ▴ 10 • written 4.6 years ago by ▴ 30
0
votes
10
replies
4.0k
views
WGCNA differences two groups 10 replicates each group
WGCNA
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by • 0
3
votes
9
replies
2.3k
views
problem for finding soft thresholding in WGCNA algorithm
wgcna abline function Scale independence diagram
5.5 years ago modarzi ▴ 10
4
votes
9
replies
3.3k
views
WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
WGCNA similarity correlation bioconductor rnaseq
updated 7.2 years ago by ★ 3.0k • written 7.3 years ago by ▴ 40
0
votes
9
replies
3.3k
views
WGCNA module trait relationship issue
wgcna
updated 3.9 years ago by ★ 3.0k • written 3.9 years ago by • 0
2
votes
9
replies
3.9k
views
Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 2.0 years ago by 41k • written 2.4 years ago by ▴ 10
7
votes
9
replies
1.3k
views
Unclear of calculating correlations with case+control samples together
WGCNA wgcna
7.5 years ago mocharrout ▴ 20
7
votes
9
replies
3.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 15 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
1
vote
8
replies
5.0k
views
Error in TOMplot (WGCNA)
WGCNA TOMplot
7.6 years ago Abhishek Singh ▴ 20
6
votes
8
replies
8.3k
views
WGCNA export to cytoscape
wgcna cytoscape
updated 6.3 years ago by ▴ 60 • written 7.0 years ago by ▴ 60
0
votes
8
replies
3.3k
views
WGCNA Soft Thresholding: Why does my y-axis for signed R^2 (R-squared) go above 1 and asymptote at 1.5?
WGCNA Soft Thresholding
updated 4.1 years ago by ★ 3.0k • written 4.1 years ago by • 0
11
votes
8
replies
8.6k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 70
5
votes
8
replies
4.5k
views
WGCNA tutorial II
WGCNA female and male datasets
updated 2.1 years ago by • 0 • written 4.0 years ago by ▴ 60
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
1
vote
8
replies
4.4k
views
WGCNA error : Error in hclust
WGCNA
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 10
9
votes
7
replies
4.1k
views
WGCNA: relate modules to binary trait
WGCNA module eigengene binary trait R
updated 5.3 years ago by ▴ 30 • written 5.3 years ago by ▴ 50
3
votes
7
replies
2.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 6.0 years ago by ★ 3.0k • written 6.0 years ago by ▴ 10
2
votes
7
replies
4.6k
views
How to create "trait data" file for WGCNA
wgcna coexpression correlation microarray
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 20
3
votes
7
replies
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
11 months ago Ortega-C ▴ 10
2
votes
7
replies
3.1k
views
WGCNA: Topological Overlap Matrix (TOM) Values Greater Than 1
WGCNA
3.6 years ago teresisc ▴ 10
5
votes
7
replies
2.7k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 5.9 years ago by ★ 3.0k • written 5.9 years ago by ▴ 10
4
votes
6
replies
1.1k
views
WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are named)
WGCNA
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 20
0
votes
6
replies
1.3k
views
RNseq data for WGCNA
WGCNA
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by ▴ 50
1
vote
6
replies
2.3k
views
WGCNA with distance matrix only from newick data.
WGCNA eigengene hub genes
6.5 years ago yifangt ▴ 20
2
votes
6
replies
4.6k
views
Error running TOMplot in WGCNA package
wgcna network
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
0
votes
6
replies
5.0k
views
WGCNA network creation error
WGCNA
updated 2.3 years ago by ★ 3.0k • written 8.7 years ago by ▴ 30
4
votes
6
replies
5.5k
views
WGCNA automatic vs manual network creation
WGCNA
updated 8.5 years ago by ★ 3.0k • written 8.5 years ago by ▴ 30
3
votes
6
replies
4.5k
views
WGCNA gene significance and module membership
WGCNA R
updated 17 months ago by ★ 3.0k • written 4.5 years ago by • 0
0
votes
6
replies
1.4k
views
Overlapping genes between gene modules in WGCNA
WGCNA
4.3 years ago shresthavivek18 • 0
0
votes
6
replies
2.3k
views
WGCNA exporting for Visant visualization
wgcna visant
updated 7.1 years ago by ★ 3.0k • written 7.1 years ago by • 0
5
votes
6
replies
6.6k
views
WGCNA - module membership via max kME?
wgcna modules
updated 6.5 years ago by ★ 3.0k • written 6.6 years ago by ▴ 10
8
votes
6
replies
4.4k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 4.6 years ago by ★ 3.0k • written 4.6 years ago by ▴ 160
0
votes
6
replies
1.7k
views
Breaking down the output from plotEigengeneNetworks()
WGCNA Heatmap EigenGeneNetworks
4.5 years ago l.s.wijaya • 0
3
votes
6
replies
838
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
6
replies
1.8k
views
RNA-Seq normalization for co-expression analysis
edger WGCNA limma
updated 4.8 years ago by 50k • written 4.8 years ago by ▴ 50
3
votes
6
replies
2.6k
views
WGCNA normalized CDF to use, WGCNA Intramodular connectivity
wgcna affymetrix microarrays affy
updated 8.8 years ago by ★ 3.0k • written 8.9 years ago by ▴ 30
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
3
votes
6
replies
1.4k
views
Questions on Pigengene
Pigengene WGCNA
updated 6.1 years ago by ▴ 200 • written 6.2 years ago by • 0
2
votes
5
replies
5.3k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna heatmap desq2 clustering
updated 9.0 years ago by ★ 1.5k • written 9.0 years ago by ▴ 250
1
vote
5
replies
3.3k
views
adjacency function of WGCNA
wgcna
7.7 years ago wlnjseu • 0
11
votes
5
replies
3.1k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 7.7 years ago by ★ 3.0k • written 7.7 years ago by ▴ 60
3
votes
5
replies
1.3k
views
Samples replications in WGCNA?
WGCNA
updated 4.0 years ago by ★ 3.9k • written 4.1 years ago by ▴ 60
4
votes
5
replies
2.2k
views
WGCNA network visualisation in RCyjs
WGCNA rcytoscape network analysis
updated 7.9 years ago by ▴ 470 • written 7.9 years ago by ▴ 20
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 14 days ago by • 0 • written 9.1 years ago by ▴ 150
0
votes
5
replies
1.4k
views
WGCNA Co-expression network analysis on cuffdiff output
WGCNA cuffdiff
5.6 years ago sbbinfo90 • 0
1
vote
5
replies
4.1k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 70
1
vote
5
replies
1.3k
views
Error in sizeRestrictedClusterMerge: replace is not a multiple of replacement length
wgcna
updated 5.0 years ago by ★ 3.0k • written 5.0 years ago by ▴ 730
3
votes
5
replies
7.3k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna rnaseq R bioconductor
updated 8.3 years ago by ★ 3.0k • written 8.3 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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