Showing : WGCNA • reset
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.4 years ago by ▴ 730 • written 7.6 years ago by ▴ 40
8
votes
17
replies
14k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA Sample Size Outliers
updated 8.6 years ago by • 0 • written 9.2 years ago by ▴ 150
14
votes
4
replies
14k
views
WGCNA Hub Gene Selection Method
WGCNA Hub Genes KmE Intramodular Connectivity
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by ▴ 150
11
votes
8
replies
8.5k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 70
6
votes
8
replies
8.3k
views
WGCNA export to cytoscape
wgcna cytoscape
updated 6.3 years ago by ▴ 60 • written 6.9 years ago by ▴ 60
0
votes
2
replies
8.0k
views
Unable to install, update WGCNA and GO.db
WGCNA software error
4.3 years ago rproendo ▴ 20
3
votes
5
replies
7.6k
views
Wgcna with missing values - error with calculation of bicor correlations in pickSoftThreshold and blockwiseModules
software error rnaseq wgcna missing data
8.4 years ago • updated 8.0 years ago dvillarlozano ▴ 10
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 6 days ago by • 0 • written 9.1 years ago by ▴ 150
3
votes
5
replies
7.3k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna rnaseq R bioconductor
updated 8.3 years ago by ★ 3.0k • written 8.3 years ago by ▴ 30
8
votes
4
replies
6.9k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by ▴ 180
5
votes
6
replies
6.6k
views
WGCNA - module membership via max kME?
wgcna modules
updated 6.5 years ago by ★ 3.0k • written 6.5 years ago by ▴ 10
1
vote
1
reply
6.2k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.1 years ago by ★ 3.0k • written 7.1 years ago by ▴ 10
4
votes
5
replies
6.2k
views
WGCNA Tutorial Selection
wgcna coexpression
updated 8.8 years ago by ★ 8.2k • written 8.9 years ago by ▴ 10
2
votes
4
replies
6.0k
views
WGCNA: 1) low soft thresholding power, 2) large modules, 3) best correlation for different types of trait variables
WGCNA
updated 4.6 years ago by ★ 3.0k • written 4.6 years ago by • 0
4
votes
6
replies
5.5k
views
WGCNA automatic vs manual network creation
WGCNA
updated 8.5 years ago by ★ 3.0k • written 8.5 years ago by ▴ 30
7
votes
3
replies
5.4k
views
WGCNA sample size minimum: why?
wgcna
updated 3.1 years ago by • 0 • written 4.8 years ago by ▴ 160
2
votes
5
replies
5.2k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna heatmap desq2 clustering
updated 9.0 years ago by ★ 1.5k • written 9.0 years ago by ▴ 250
3
votes
2
replies
5.0k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 23 months ago by ▴ 10 • written 3.7 years ago by ▴ 80
0
votes
6
replies
5.0k
views
WGCNA network creation error
WGCNA
updated 2.2 years ago by ★ 3.0k • written 8.7 years ago by ▴ 30
1
vote
8
replies
5.0k
views
Error in TOMplot (WGCNA)
WGCNA TOMplot
7.6 years ago • updated 7.5 years ago Abhishek Singh ▴ 20
11
votes
3
replies
4.9k
views
WGCNA - Signed vs signed hybrid networks
wgcna
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 20
2
votes
2
replies
4.9k
views
WGCNA extract genes from a module
WGCNA wgcna package
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 10
2
votes
3
replies
4.7k
views
WGCNA "bicor" correlation
wgcna bicor WGCNA
8.5 years ago bcbio_uk ▴ 10
2
votes
6
replies
4.6k
views
Error running TOMplot in WGCNA package
wgcna network
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
2
votes
7
replies
4.6k
views
How to create "trait data" file for WGCNA
wgcna coexpression correlation microarray
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 20
13
votes
1
reply
4.6k
views
WGCNA - Compare module preservation between class
WGCNA coexpression
updated 8.7 years ago by ★ 3.0k • written 8.7 years ago by ▴ 60
1
vote
12
replies
4.5k
views
WGCNA: correlations module-traits, and module membership-gene significance
WGCNA co-expression analysis gene significance module membership module-trait relationship
updated 22 months ago by ▴ 10 • written 4.6 years ago by ▴ 30
2
votes
4
replies
4.5k
views
WGCNA: intrepreting grey unassigned "module"?
WGCNA rnaseq gene expression co-expression network
updated 6.0 years ago by ★ 3.0k • written 6.0 years ago by ▴ 10
6
votes
2
replies
4.5k
views
WGCNA: how to change module color
wgcna
updated 5.6 years ago by ★ 3.0k • written 5.6 years ago by ▴ 20
3
votes
6
replies
4.5k
views
WGCNA gene significance and module membership
WGCNA R
updated 17 months ago by ★ 3.0k • written 4.4 years ago by • 0
5
votes
8
replies
4.4k
views
WGCNA tutorial II
WGCNA female and male datasets
updated 2.1 years ago by • 0 • written 4.0 years ago by ▴ 60
8
votes
6
replies
4.4k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 4.6 years ago by ★ 3.0k • written 4.6 years ago by ▴ 160
1
vote
8
replies
4.3k
views
WGCNA error : Error in hclust
WGCNA
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 10
1
vote
2
replies
4.3k
views
WGCNA distance measures, clustering with TOM based on adjacency matrix type = "distance" versus correlation
wgcna microarray clustering
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by • 0
2
votes
2
replies
4.3k
views
How to select mergeCutHeight in WGCNA?
WGCNA mergeCutHeight
updated 6.3 years ago by ★ 3.0k • written 6.3 years ago by ▴ 60
9
votes
2
replies
4.2k
views
Filtering low variance genes for WGCNA
deseq2 WGCNA
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by ▴ 30
2
votes
3
replies
4.2k
views
WGCNA TOMType specification
WGCNA network analysis Sign
6.6 years ago • updated 6.0 years ago aurora.savino ▴ 10
9
votes
7
replies
4.1k
views
WGCNA: relate modules to binary trait
WGCNA module eigengene binary trait R
updated 5.3 years ago by ▴ 30 • written 5.3 years ago by ▴ 50
5
votes
2
replies
4.1k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by ▴ 30
0
votes
2
replies
4.1k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 10
1
vote
5
replies
4.1k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 70
4
votes
2
replies
4.0k
views
Selecting genes based on expressional variance
geneexpression wgcna rnaseq
updated 9.6 years ago by 1.6k • written 9.6 years ago by ▴ 250
1
vote
2
replies
4.0k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
0
votes
10
replies
4.0k
views
WGCNA differences two groups 10 replicates each group
WGCNA
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by • 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
0
votes
4
replies
3.9k
views
WGCNA grey module
WGCNA
updated 12 months ago by ▴ 10 • written 5.9 years ago by ▴ 10
2
votes
9
replies
3.9k
views
Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 24 months ago by 41k • written 2.3 years ago by ▴ 10
12
votes
4
replies
3.8k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by ▴ 30
1
vote
1
reply
3.7k
views
WGCNA - signedKME function
WGCNA RNA-seq signedKME
updated 9.3 years ago by ★ 3.0k • written 9.3 years ago by ▴ 10
10
votes
1
reply
3.7k
views
WGCNA: Module preservation vs consensus analysis
WGCNA wgcna
updated 3.1 years ago by ▴ 70 • written 3.2 years ago by ▴ 60
50 results • Page 1 of 1
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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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