Showing : wgcna • reset
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
3 days ago k200987 • 0
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5
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1.7k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 13 months ago by • 0
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2
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207
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
6 weeks ago Gimena • 0
0
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2
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242
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
7 weeks ago • updated 6 weeks ago w.cookson • 0
0
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1
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184
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problem with ClusterRepro function
WGCNA
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
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1
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318
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
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2
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560
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 5 months ago by • 0
4
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3
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1.0k
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WGCNA documentation not available
WGCNA
written 5 months ago by ▴ 10
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2
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948
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 3 days ago by • 0 • written 18 months ago by • 0
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1
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1.0k
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WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 5 months ago by • 0 • written 2.4 years ago by • 0
1
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2
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699
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
5 months ago • updated 4 months ago Levi • 0
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2
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325
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
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1
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529
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
1
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1
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425
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by ▴ 190 • written 6 months ago by ▴ 10
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1
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408
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
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1
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2.1k
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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 9 months ago by 65k • written 9 months ago by • 0
1
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1
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509
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
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1
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642
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 11 months ago by ★ 4.1k • written 11 months ago by ▴ 20
2
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5
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1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 4 weeks ago by • 0 • written 11 months ago by • 0
3
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6
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861
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
1
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0
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491
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 42k • written 11 months ago by ▴ 20
2
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1
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525
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 11 months ago by ▴ 50 • written 11 months ago by ▴ 10
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0
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439
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
12 months ago Levi • 0
0
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1
reply
901
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 11 weeks ago by ▴ 720 • written 15 months ago by • 0
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2
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1.3k
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WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna WGCNA
written 2.1 years ago by • 0
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1
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1.1k
views
WGCNA Preservation error
preservation WGCNA
updated 3 months ago by • 0 • written 2.4 years ago by • 0
6
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6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.1 years ago by ▴ 60
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2
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828
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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 4 months ago by • 0 • written 4.6 years ago by • 0
5
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8
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3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
11
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5
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7.4k
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Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 4 weeks ago by • 0 • written 9.2 years ago by ▴ 150
30 results • Page 1 of 1
Recent ...
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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