Showing : WGCNA • reset
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
13 days ago • updated 12 days ago Gimena • 0
0
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2
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194
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
18 days ago • updated 13 days ago w.cookson • 0
0
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1
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151
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problem with ClusterRepro function
WGCNA
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
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1
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221
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
0
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2
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459
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by • 0
4
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3
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810
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WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
1
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2
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632
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago • updated 3 months ago Levi • 0
0
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2
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291
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WGCNA less samples
RNA-Seq WGCNA Worms
4 months ago davca • 0
0
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1
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467
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
1
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1
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373
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 5 months ago by ▴ 190 • written 5 months ago by ▴ 10
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1
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370
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
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1
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1.8k
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Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 8 months ago by 65k • written 8 months ago by • 0
1
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1
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474
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
0
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1
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572
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 20
2
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4
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 4 months ago by • 0 • written 10 months ago by • 0
3
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6
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808
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 months ago by ▴ 10
1
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0
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448
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 10 months ago by ▴ 20
2
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1
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484
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 10 months ago by ▴ 50 • written 10 months ago by ▴ 10
0
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0
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404
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
10 months ago Levi • 0
3
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7
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1.1k
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"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
0
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1
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510
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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
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0
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525
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
11 months ago Ortega-C ▴ 10
0
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2
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581
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WGCNA problem
WGCNA
updated 11 months ago by ▴ 10 • written 12 months ago by • 0
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4
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1.5k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 7 weeks ago by • 0 • written 12 months ago by • 0
0
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1
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854
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 6 weeks ago by ▴ 720 • written 14 months ago by • 0
0
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1
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845
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 months ago by • 0 • written 16 months ago by • 0
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2
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1.3k
views
WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna WGCNA
written 2.0 years ago by • 0
0
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1
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1.0k
views
WGCNA Preservation error
preservation WGCNA
updated 12 weeks ago by • 0 • written 2.3 years ago by • 0
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1
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975
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WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 4 months ago by • 0 • written 2.3 years ago by • 0
6
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6
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2.6k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
0
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2
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785
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Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA Module Detection
updated 12 weeks ago by • 0 • written 4.5 years ago by • 0
5
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8
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3.9k
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Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
1
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2
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2.6k
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WGNCA kME vs. kIM
WGCNA
updated 11 months ago by • 0 • written 8.6 years ago by ▴ 30
11
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4
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7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 19 days ago by ★ 3.0k • written 9.1 years ago by ▴ 150
34 results • Page 1 of 1
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Replies
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Comment: [DiffBind] Obtaining normalization factors by Henry ▴ 10
I see, thank you for your suggestion! I managed to use a separate RLE normalization to obtain the size factors.
Answer: Memory errors using read.bismark? by Peter Hickey ▴ 690
Thanks for sharing an example file. This is a very large non-CpG methylation dataset, which are tricky to work with for a number of reason…
Votes
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
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