Showing : wgcna • reset
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5.5k
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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
183
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wgcna module preseravtion taking too long?
WGCNA
updated 17 days ago by ★ 5.0k • written 23 days ago by • 0
1
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2
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382
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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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726
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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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8.2k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.4 years ago by ▴ 80
0
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5
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950
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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
views
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
962
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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4.8k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 10 months ago by • 0 • written 9.4 years ago by ▴ 60
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1
reply
824
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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
650
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
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2
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606
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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
votes
1
reply
372
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
0
votes
1
reply
768
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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495
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WGCNA module preservation using only adjacency matrix
WGCNA
14 months ago yang1641 • 0
3
votes
4
replies
1.7k
views
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
reply
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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633
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
15 months ago Fernanda • 0
0
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1
reply
676
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
699
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 16 months ago by 68k • written 16 months ago by • 0
1
vote
3
replies
4.6k
views
WGNCA kME vs. kIM
WGCNA
updated 19 months ago by • 0 • written 10.3 years ago by ▴ 30
0
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0
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560
views
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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929
views
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
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
21 months ago w.cookson • 0
0
votes
1
reply
728
views
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
views
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
replies
3.1k
views
WGCNA documentation not available
WGCNA
written 2.1 years ago by ▴ 10
0
votes
2
replies
2.6k
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
vote
2
replies
1.9k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.1 years ago • updated 2.0 years ago Levi • 0
0
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2
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859
views
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
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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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874
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
votes
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
vote
1
reply
976
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.5 years ago by ★ 5.0k • written 2.5 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
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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
replies
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
reply
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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846
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.6 years ago Levi • 0
3
votes
7
replies
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
930
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
views
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
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0
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825
views
Module Trait Corelation
WGCNA
2.8 years ago allanokwaro • 0
2
votes
3
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1.9k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 20
336 results • Page 1 of 7
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Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa by Gordon Smyth 53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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