Showing : WGCNA • reset
0
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5.7k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 2.8 years ago by • 0
0
votes
1
reply
298
views
wgcna module preseravtion taking too long?
WGCNA
updated 6 weeks ago by ★ 5.0k • written 7 weeks ago by • 0
1
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2
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416
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 5 months ago by ▴ 20
0
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4
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841
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Issue with Soft-Thresholding in WGCNA
WGCNA
written 10 months ago by • 0
3
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4
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8.5k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.5 years ago by ▴ 80
0
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5
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1.1k
views
WGCNA
WGCNA Normalization RNASeq
written 11 months ago by • 0
6
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8
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6.0k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.8 years ago by ▴ 60
0
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1
reply
1.0k
views
WGCNA
WGCNA DESeq2
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
11
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6
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5.0k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 11 months ago by • 0 • written 9.5 years ago by ▴ 60
0
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1
reply
911
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
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1
reply
730
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
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2
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692
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
12 months ago Vinesh • 0
0
votes
1
reply
385
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
votes
1
reply
814
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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0
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546
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WGCNA module preservation using only adjacency matrix
WGCNA
15 months ago yang1641 • 0
3
votes
4
replies
1.8k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
16 months ago sukeshinik5 ▴ 20
1
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1
reply
1.0k
views
WGCNA
DEGselection RNASeqData WGCNA
updated 16 months ago by ▴ 760 • written 16 months ago by • 0
0
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0
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665
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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
795
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 17 months ago by ▴ 760 • written 17 months ago by • 0
0
votes
1
reply
783
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
3
replies
4.8k
views
WGNCA kME vs. kIM
WGCNA
updated 20 months ago by • 0 • written 10.4 years ago by ▴ 30
0
votes
0
replies
596
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
21 months ago k200987 • 0
0
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2
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986
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
22 months ago Gimena • 0
0
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2
replies
1.1k
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
22 months ago w.cookson • 0
0
votes
1
reply
751
views
problem with ClusterRepro function
WGCNA
updated 23 months ago by 68k • written 23 months ago by • 0
0
votes
1
reply
1.4k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
0
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2
replies
1.8k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 2.2 years ago by • 0
4
votes
3
replies
3.2k
views
WGCNA documentation not available
WGCNA
written 2.2 years ago by ▴ 10
0
votes
2
replies
2.9k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 21 months ago by • 0 • written 3.2 years ago by • 0
0
votes
1
reply
1.7k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 2.2 years ago by • 0 • written 4.2 years ago by • 0
1
vote
2
replies
2.0k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.2 years ago • updated 2.1 years ago Levi • 0
0
votes
2
replies
881
views
WGCNA less samples
RNA-Seq WGCNA Worms
2.2 years ago davca • 0
0
votes
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
replies
1.4k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.3 years ago by ▴ 10
0
votes
1
reply
894
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
1
reply
5.2k
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
vote
1
reply
997
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
2.5k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 22 months ago by • 0 • written 2.7 years ago by • 0
3
votes
6
replies
1.7k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
1
vote
0
replies
1.1k
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 20
2
votes
1
reply
1.2k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 2.7 years ago by ▴ 50 • written 2.7 years ago by ▴ 10
0
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0
replies
883
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.7 years ago Levi • 0
3
votes
7
replies
2.8k
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
votes
1
reply
950
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
votes
0
replies
1.1k
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
2.8 years ago Ortega-C ▴ 10
0
votes
2
replies
1.2k
views
WGCNA problem
WGCNA
updated 2.8 years ago by ▴ 10 • written 2.8 years ago by • 0
0
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0
replies
1.0k
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.8 years ago Levi • 0
0
votes
0
replies
844
views
Module Trait Corelation
WGCNA
2.9 years ago allanokwaro • 0
2
votes
3
replies
1.9k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 20
336 results • Page 1 of 7
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To resolve technical errors like installation failures or login issues, first ensure your device allows in the security settings and that…
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Votes
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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