Showing : wgcna • reset
8
votes
17
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14k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA Sample Size Outliers
updated 8.6 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
4.5k
views
WGCNA: correlations module-traits, and module membership-gene significance
WGCNA co-expression analysis gene significance module membership module-trait relationship
updated 22 months ago by ▴ 10 • written 4.6 years ago by ▴ 30
0
votes
10
replies
3.9k
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
2.2k
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 7.2 years ago by ▴ 40
0
votes
9
replies
3.2k
views
WGCNA module trait relationship issue
wgcna
updated 3.8 years ago by ★ 3.0k • written 3.8 years ago by • 0
2
votes
9
replies
3.8k
views
Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 23 months ago by 41k • written 2.3 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
3.6k
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
7.5 years ago Abhishek Singh ▴ 20
6
votes
8
replies
8.2k
views
WGCNA export to cytoscape
wgcna cytoscape
updated 6.3 years ago by ▴ 60 • written 6.9 years ago by ▴ 60
0
votes
8
replies
3.2k
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
8.5k
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
4.4k
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 7.1 years ago by ▴ 40
1
vote
8
replies
4.3k
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
1.1k
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
3.0k
views
WGCNA: Topological Overlap Matrix (TOM) Values Greater Than 1
WGCNA
3.5 years ago teresisc ▴ 10
5
votes
7
replies
2.7k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 5.8 years ago by ★ 3.0k • written 5.8 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 5.1 years ago by ★ 3.0k • written 5.1 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
6.4 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 2.2 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 4.4 years ago by • 0
0
votes
6
replies
1.3k
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 7.0 years ago by ★ 3.0k • written 7.0 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 6.5 years ago by ▴ 10
8
votes
6
replies
4.4k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 4.5 years ago by ★ 3.0k • written 4.6 years ago by ▴ 160
0
votes
6
replies
1.6k
views
Breaking down the output from plotEigengeneNetworks()
WGCNA Heatmap EigenGeneNetworks
4.5 years ago l.s.wijaya • 0
3
votes
6
replies
814
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 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
5.2k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna heatmap desq2 clustering
updated 8.9 years ago by ★ 1.5k • written 8.9 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
1.2k
views
Samples replications in WGCNA?
WGCNA
updated 4.0 years ago by ★ 3.9k • written 4.0 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
7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 19 hours 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
4.0k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 7.5 years ago by ★ 3.0k • written 7.5 years ago by ▴ 70
1
vote
5
replies
1.3k
views
Error in sizeRestrictedClusterMerge: replace is not a multiple of replacement length
wgcna
updated 4.9 years ago by ★ 3.0k • written 4.9 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: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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