Showing : WGCNA • reset
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
8
votes
17
replies
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
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 7.7 years ago by ★ 3.0k • written 7.7 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
7
votes
9
replies
1.3k
views
Unclear of calculating correlations with case+control samples together
WGCNA wgcna
7.5 years ago mocharrout ▴ 20
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
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
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
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
1
vote
8
replies
4.9k
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
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
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
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
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
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
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
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
2
votes
7
replies
3.0k
views
WGCNA: Topological Overlap Matrix (TOM) Values Greater Than 1
WGCNA
3.5 years ago teresisc ▴ 10
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
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
6
votes
6
replies
2.6k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
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
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
0
votes
6
replies
1.3k
views
Overlapping genes between gene modules in WGCNA
WGCNA
4.3 years ago shresthavivek18 • 0
3
votes
6
replies
4.4k
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
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
4.3k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 4.5 years ago by ★ 3.0k • written 4.5 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
809
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 8.7 years ago by ★ 3.0k • written 8.9 years ago by ▴ 30
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 • updated 7.6 years ago wlnjseu • 0
11
votes
5
replies
3.1k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 60
4
votes
5
replies
2.2k
views
WGCNA network visualisation in RCyjs
WGCNA rcytoscape network analysis
updated 7.8 years ago by ▴ 470 • written 7.9 years ago by ▴ 20
1
vote
5
replies
1.5k
views
Need comments/advices for WGCNA network visualization
WGCNA
4.0 years ago minyaaa9058 ▴ 30
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
3
votes
5
replies
7.6k
views
Wgcna with missing values - error with calculation of bicor correlations in pickSoftThreshold and blockwiseModules
software error rnaseq wgcna missing data
8.3 years ago • updated 8.0 years ago dvillarlozano ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: DEG with low counts by Rajat • 0
Dear Dr. Michael Thanks for you quick reply. I appreciate it. Attached is the plotcounts for one gene. I am experiencing like this in oth…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for your guide! I check my data as you said there is no difference in my data. This is the MDS plot at genes l…
Comment: How to correct for known and surrogate variables in DESeq2? by Michael Love 41k
To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error by shepherl 3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2? by nhaus ▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Votes
Answer: Light difference when using coef vs omit a group when compare 3 groups.
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
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