Showing : WGCNA • reset
4
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3
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860
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WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
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
0
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2
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484
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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
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
0
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5
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1.6k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
11
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5
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7.3k
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Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 6 days ago by • 0 • written 9.1 years ago by ▴ 150
0
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2
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212
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
27 days ago • updated 22 days ago w.cookson • 0
0
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2
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169
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
22 days ago • updated 21 days ago Gimena • 0
6
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6
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2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
0
votes
1
reply
478
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
0
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1
reply
986
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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 2.4 years ago by • 0
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 7 days ago by • 0 • written 10 months ago by • 0
3
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7
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1.2k
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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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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 9 months ago by 65k • written 9 months ago by • 0
0
votes
1
reply
591
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 20
0
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2
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300
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
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1
reply
867
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 months ago by • 0 • written 17 months ago by • 0
1
vote
1
reply
481
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
3
votes
6
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829
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 11 months ago by ▴ 10
0
votes
1
reply
379
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
0
votes
1
reply
161
views
problem with ClusterRepro function
WGCNA
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
1
vote
1
reply
389
views
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
0
votes
0
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535
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
12 months ago Ortega-C ▴ 10
1
vote
2
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649
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago Levi • 0
1
vote
0
replies
460
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 11 months ago by ▴ 20
0
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1
reply
865
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 7 weeks ago by ▴ 720 • written 14 months ago by • 0
0
votes
1
reply
517
views
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
votes
1
reply
243
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 10 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
0
votes
2
replies
797
views
Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA Module Detection
updated 3 months ago by • 0 • written 4.5 years ago by • 0
0
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0
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415
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
0
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1
reply
1.0k
views
WGCNA Preservation error
preservation WGCNA
updated 3 months ago by • 0 • written 2.3 years ago by • 0
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
2
votes
1
reply
496
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 10 months ago by ▴ 50 • written 11 months ago by ▴ 10
33 results • Page 1 of 1
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Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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