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WGCNA
•
reset
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
mh.manoj
• 0 • written 9.2 years ago by
brohawndg
▴ 150
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.4 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.6 years ago by
jol.espinoz
▴ 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 22 months ago by
annamariabugaj
▴ 10 • written 4.6 years ago by
rodrigo.duarte88
▴ 30
0
votes
10
replies
4.0k
views
WGCNA differences two groups 10 replicates each group
WGCNA
updated 7.8 years ago by
Peter Langfelder
★ 3.0k • written 7.8 years ago by
nicky.driedonks
• 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
Peter Langfelder
★ 3.0k • written 7.2 years ago by
jol.espinoz
▴ 40
0
votes
9
replies
3.3k
views
WGCNA module trait relationship issue
wgcna
updated 3.8 years ago by
Peter Langfelder
★ 3.0k • written 3.8 years ago by
zen
• 0
2
votes
9
replies
3.9k
views
Deseq2 normalization for WGCNA
RNASeq
Deseq2
DESeq2
WGCNA
updated 24 months ago by
Michael Love
41k • written 2.3 years ago by
jms2520
▴ 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
Peter Langfelder
★ 3.0k • written 5.0 years ago by
avelarbio46
▴ 10
1
vote
8
replies
5.0k
views
Error in TOMplot (WGCNA)
WGCNA
TOMplot
7.6 years ago • updated 7.5 years ago
Abhishek Singh
▴ 20
6
votes
8
replies
8.3k
views
WGCNA export to cytoscape
wgcna
cytoscape
updated 6.3 years ago by
harelarik
▴ 60 • written 7.0 years ago by
2323982403
▴ 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
Peter Langfelder
★ 3.0k • written 4.1 years ago by
DWF
• 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
Peter Langfelder
★ 3.0k • written 7.6 years ago by
gokce.ouz
▴ 70
5
votes
8
replies
4.5k
views
WGCNA tutorial II
WGCNA
female and male datasets
updated 2.1 years ago by
synat.keam
• 0 • written 4.0 years ago by
bahmanik@msu.edu
▴ 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
panagiotis.mokos
▴ 40
1
vote
8
replies
4.4k
views
WGCNA error : Error in hclust
WGCNA
updated 7.3 years ago by
Peter Langfelder
★ 3.0k • written 7.3 years ago by
lwang.daniel
▴ 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
pedrostrusso
▴ 30 • written 5.3 years ago by
Lin
▴ 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
Peter Langfelder
★ 3.0k • written 6.0 years ago by
7kemZmani
▴ 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
Peter Langfelder
★ 3.0k • written 8.2 years ago by
shalinisonar13
▴ 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
3.0k
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
Peter Langfelder
★ 3.0k • written 5.8 years ago by
modarzi
▴ 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
Peter Langfelder
★ 3.0k • written 5.2 years ago by
cats_dogs
▴ 20
0
votes
6
replies
1.3k
views
RNseq data for WGCNA
WGCNA
updated 6.6 years ago by
Peter Langfelder
★ 3.0k • written 6.6 years ago by
joseph
▴ 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
Keith Hughitt
▴ 180 • written 9.6 years ago by
Jon Bråte
▴ 250
0
votes
6
replies
5.0k
views
WGCNA network creation error
WGCNA
updated 2.2 years ago by
Peter Langfelder
★ 3.0k • written 8.7 years ago by
akridgerunner
▴ 30
4
votes
6
replies
5.5k
views
WGCNA automatic vs manual network creation
WGCNA
updated 8.5 years ago by
Peter Langfelder
★ 3.0k • written 8.5 years ago by
akridgerunner
▴ 30
3
votes
6
replies
4.5k
views
WGCNA gene significance and module membership
WGCNA
R
updated 17 months ago by
Peter Langfelder
★ 3.0k • written 4.5 years ago by
VictoriaL
• 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
Peter Langfelder
★ 3.0k • written 7.1 years ago by
arom2
• 0
5
votes
6
replies
6.6k
views
WGCNA - module membership via max kME?
wgcna
modules
updated 6.5 years ago by
Peter Langfelder
★ 3.0k • written 6.5 years ago by
ly.leifels
▴ 10
8
votes
6
replies
4.4k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 4.6 years ago by
Peter Langfelder
★ 3.0k • written 4.6 years ago by
charles.foster
▴ 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
832
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
2
votes
6
replies
1.8k
views
RNA-Seq normalization for co-expression analysis
edger
WGCNA
limma
updated 4.8 years ago by
Gordon Smyth
50k • written 4.8 years ago by
Lin
▴ 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
Peter Langfelder
★ 3.0k • written 8.9 years ago by
akridgerunner
▴ 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
Colari19
▴ 60
3
votes
6
replies
1.4k
views
Questions on Pigengene
Pigengene
WGCNA
updated 6.1 years ago by
Habil Zare
▴ 200 • written 6.2 years ago by
boting.m.ning
• 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 9.0 years ago by
Dario Strbenac
★ 1.5k • written 9.0 years ago by
Jon Bråte
▴ 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
Peter Langfelder
★ 3.0k • written 7.7 years ago by
2323982403
▴ 60
3
votes
5
replies
1.2k
views
Samples replications in WGCNA?
WGCNA
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
bahmanik@msu.edu
▴ 60
4
votes
5
replies
2.2k
views
WGCNA network visualisation in RCyjs
WGCNA
rcytoscape
network analysis
updated 7.9 years ago by
Paul Shannon
▴ 470 • written 7.9 years ago by
christopher.clarskon15
▴ 20
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 7 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 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
Peter Langfelder
★ 3.0k • written 7.6 years ago by
gokce.ouz
▴ 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
Peter Langfelder
★ 3.0k • written 4.9 years ago by
Lluís Revilla Sancho
▴ 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
Peter Langfelder
★ 3.0k • written 8.3 years ago by
sm15766
▴ 30
50 results • Page
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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