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
votes
1
reply
299
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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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418
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 6 months ago by ▴ 20
0
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4
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843
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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
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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
918
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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
732
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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695
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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
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1
reply
386
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
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1
reply
820
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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554
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WGCNA module preservation using only adjacency matrix
WGCNA
15 months ago yang1641 • 0
3
votes
4
replies
1.9k
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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667
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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
799
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
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0
replies
600
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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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994
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
22 months ago Gimena • 0
0
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2
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1.1k
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
22 months ago w.cookson • 0
0
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1
reply
753
views
problem with ClusterRepro function
WGCNA
updated 23 months ago by 68k • written 23 months ago by • 0
0
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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
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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
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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
2.1k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.2 years ago • updated 2.1 years ago Levi • 0
0
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2
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882
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WGCNA less samples
RNA-Seq WGCNA Worms
2.2 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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1.4k
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
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1
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898
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
999
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
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0
replies
1.1k
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.7 years ago by 43k • written 2.7 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 2.7 years ago by ▴ 50 • written 2.7 years ago by ▴ 10
0
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0
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883
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.7 years ago Levi • 0
3
votes
7
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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
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1
reply
952
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
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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
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2
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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
1.1k
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.8 years ago Levi • 0
0
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0
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845
views
Module Trait Corelation
WGCNA
2.9 years ago allanokwaro • 0
2
votes
3
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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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All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
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In my experience, the within-clone variability of differentiated stem cells is often as large or larger than the between-clone variability,…
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Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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