Showing : WGCNA • reset
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.8 years ago by • 0
0
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1
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225
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wgcna module preseravtion taking too long?
WGCNA
updated 22 days ago by ★ 5.0k • written 29 days ago by • 0
1
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2
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392
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 5 months ago by ▴ 20
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4
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742
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Issue with Soft-Thresholding in WGCNA
WGCNA
written 9 months ago by • 0
3
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4
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8.3k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.4 years ago by ▴ 80
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5
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968
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WGCNA
WGCNA Normalization RNASeq
written 10 months ago by • 0
6
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8
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5.8k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.7 years ago by ▴ 60
0
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1
reply
980
views
WGCNA
WGCNA DESeq2
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
11
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6
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4.9k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 10 months ago by • 0 • written 9.4 years ago by ▴ 60
0
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1
reply
840
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
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1
reply
664
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 11 months ago by ★ 5.0k • written 12 months ago by • 0
0
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2
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624
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
11 months ago Vinesh • 0
0
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1
reply
374
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
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1
reply
777
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
0
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0
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501
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WGCNA module preservation using only adjacency matrix
WGCNA
14 months ago yang1641 • 0
3
votes
4
replies
1.7k
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
15 months ago sukeshinik5 ▴ 20
1
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1
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1.0k
views
WGCNA
DEGselection RNASeqData WGCNA
updated 15 months ago by ▴ 760 • written 15 months ago by • 0
0
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0
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639
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
16 months ago Fernanda • 0
0
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1
reply
692
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 16 months ago by ▴ 760 • written 16 months ago by • 0
0
votes
1
reply
714
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 16 months ago by 68k • written 16 months ago by • 0
1
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3
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4.6k
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WGNCA kME vs. kIM
WGCNA
updated 20 months ago by • 0 • written 10.3 years ago by ▴ 30
0
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0
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568
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
20 months ago k200987 • 0
0
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2
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942
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
21 months ago Gimena • 0
0
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2
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1.0k
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
21 months ago w.cookson • 0
0
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1
reply
730
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problem with ClusterRepro function
WGCNA
updated 22 months ago by 68k • written 22 months ago by • 0
0
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1
reply
1.4k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
0
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2
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1.8k
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 2.1 years ago by • 0
4
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3
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3.2k
views
WGCNA documentation not available
WGCNA
written 2.1 years ago by ▴ 10
0
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2
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2.7k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 20 months ago by • 0 • written 3.1 years ago by • 0
0
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1
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1.7k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 2.1 years ago by • 0 • written 4.1 years ago by • 0
1
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2
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1.9k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.1 years ago Levi • 0
0
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2
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863
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WGCNA less samples
RNA-Seq WGCNA Worms
2.1 years ago davca • 0
0
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1
reply
1.1k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
1
vote
2
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1.3k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.2 years ago by ▴ 10
0
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1
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876
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
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1
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5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
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1
reply
981
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
votes
1
reply
1.5k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 20
2
votes
5
replies
2.4k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 21 months ago by • 0 • written 2.6 years ago by • 0
3
votes
6
replies
1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
1
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0
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1.1k
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.6 years ago by 43k • written 2.6 years ago by ▴ 20
2
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1
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1.2k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 2.6 years ago by ▴ 50 • written 2.6 years ago by ▴ 10
0
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0
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858
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.6 years ago Levi • 0
3
votes
7
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2.6k
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
2.7 years ago Ortega-C ▴ 10
0
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1
reply
931
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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0
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1.0k
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
2.7 years ago Ortega-C ▴ 10
0
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2
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1.2k
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WGCNA problem
WGCNA
updated 2.7 years ago by ▴ 10 • written 2.7 years ago by • 0
0
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0
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1.0k
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.8 years ago Levi • 0
0
votes
0
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828
views
Module Trait Corelation
WGCNA
2.8 years ago allanokwaro • 0
2
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3
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1.9k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 20
336 results • Page 1 of 7
Recent ...
Replies
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
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Commentator to James W. MacDonald 68k
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