Showing : WGCNA • reset
5
votes
8
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3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
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
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
833
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
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 9 days ago by • 0 • written 10 months ago by • 0
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 7 days ago by • 0 • written 9.1 years ago by ▴ 150
4
votes
3
replies
872
views
WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
0
votes
2
replies
174
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
23 days ago • updated 22 days ago Gimena • 0
1
vote
2
replies
2.6k
views
WGNCA kME vs. kIM
WGCNA
updated 11 months ago by • 0 • written 8.6 years ago by ▴ 30
0
votes
2
replies
800
views
Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA Module Detection
updated 3 months ago by • 0 • written 4.5 years ago by • 0
1
vote
2
replies
654
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago Levi • 0
0
votes
2
replies
1.3k
views
WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna WGCNA
written 2.1 years ago by • 0
0
votes
2
replies
302
views
WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
votes
2
replies
214
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
28 days ago • updated 23 days ago w.cookson • 0
0
votes
2
replies
489
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by • 0
0
votes
1
reply
1.8k
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
0
votes
1
reply
163
views
problem with ClusterRepro function
WGCNA
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
1
reply
988
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 4 months ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
519
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 11 months ago by ★ 4.0k • written 11 months ago by • 0
0
votes
1
reply
593
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 20
0
votes
1
reply
480
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
0
votes
1
reply
875
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 months ago by • 0 • written 17 months ago by • 0
1
vote
1
reply
394
views
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
1
vote
1
reply
489
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
votes
1
reply
869
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 8 weeks ago by ▴ 720 • written 14 months ago by • 0
0
votes
1
reply
247
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 11 weeks ago by ★ 4.0k • written 11 weeks ago by • 0
0
votes
1
reply
1.0k
views
WGCNA Preservation error
preservation WGCNA
updated 3 months ago by • 0 • written 2.3 years ago by • 0
2
votes
1
reply
499
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
votes
1
reply
381
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
0
votes
0
replies
539
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
12 months ago Ortega-C ▴ 10
1
vote
0
replies
462
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 11 months ago by ▴ 20
0
votes
0
replies
418
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
33 results • Page 1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
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.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
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?
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