Showing : WGCNA • reset
1
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Evaluating Hub genes in WGCNA and role of using Signed network
rnaseq WGCNA
7.3 years ago dorothy.jrobbert ▴ 30
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0
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3.1k
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Use of bicor in WGCNA
WGCNA wgcna package wgcna bicor
7.3 years ago bekah ▴ 40
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0
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1.3k
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problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
wgcna RNA-seq Topological Overlap Matrix
7.4 years ago modarzi ▴ 10
5
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7
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3.4k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 7.4 years ago by ★ 3.0k • written 7.4 years ago by ▴ 10
0
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4
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5.9k
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WGCNA grey module
WGCNA
updated 2.6 years ago by ▴ 10 • written 7.5 years ago by ▴ 10
0
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0
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844
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WGCNA , value of nPermutations, module preservation
wgcna
7.5 years ago amnahsiddiqa ▴ 10
0
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0
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946
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WGCNA module trait relationship
WGCNA wgcna
7.5 years ago amnahsiddiqa ▴ 10
1
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1
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1.6k
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Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
0
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1
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842
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WGCNA Analysis and Hub gene analysis
wgcna
7.5 years ago nazia • 0
2
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3
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5.7k
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WGCNA TOMType specification
WGCNA network analysis Sign
8.2 years ago • updated 7.5 years ago aurora.savino ▴ 10
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0
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931
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Comparable network visualisation of consensus modules between two species
WGCNA VisANT network visualization
7.6 years ago Ira ▴ 10
2
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4
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6.0k
views
WGCNA: intrepreting grey unassigned "module"?
WGCNA rnaseq gene expression co-expression network
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 10
3
votes
7
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3.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq WGCNA deseq method coexpression
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 10
0
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0
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1.2k
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Drop of soft-threshold curve with high power values
wgcna picksoftthreshold scale-free topology co-expression network
7.6 years ago marcantoine.guery • 0
1
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1
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1.3k
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Error with the tutorial for the WGCNA package
wgcna
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 10
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0
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1.2k
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Principle in selecting the "appropriate" merging value for module generation
wgcna module mergecutheight coexpression
7.6 years ago tarun2 • 0
2
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0
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2.5k
views
'Error in summary(lm1)$coefficients[2, 1] : subscript out of bounds' while running pickSoftThreshold in WGCNA
wgcna picksoftthreshold
7.6 years ago aditi ▴ 20
3
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6
replies
2.0k
views
Questions on Pigengene
Pigengene WGCNA
updated 7.7 years ago by ▴ 200 • written 7.7 years ago by • 0
0
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0
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2.3k
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How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna modules coexpression networks
7.7 years ago jol.espinoz ▴ 40
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0
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1.2k
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How to define the top 100 hub genes in each module and find out the genes having direct connections with hub genes
WGCNA co-expression network RNA-Seq
7.7 years ago wangdp123 • 0
0
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2
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2.0k
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GOenrichmentAnalysis of WGCNA mocules in Zea mays
annotation wgcna package
7.7 years ago j.baldauf • 0
2
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1
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2.0k
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How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna coexpression transcriptome
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 40
0
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0
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1.8k
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
7.8 years ago jol.espinoz ▴ 40
1
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1
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2.6k
views
WGCNA - Choosing the best threshold
wgcna sft picksoftthreshold threshold rnaseq
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 40
2
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0
replies
3.0k
views
WGCNA package : identification of hub genes
wgcna
7.8 years ago bharata1803 ▴ 60
2
votes
2
replies
6.1k
views
How to select mergeCutHeight in WGCNA?
WGCNA mergeCutHeight
updated 7.9 years ago by ★ 3.0k • written 7.9 years ago by ▴ 60
6
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8
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11k
views
WGCNA export to cytoscape
wgcna cytoscape
updated 7.9 years ago by ▴ 60 • written 8.5 years ago by ▴ 60
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0
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2.1k
views
How to keep track of gene names during WGCNA analysis for cutTreedynamic() and moduleEigengene()?
WGCNA cbind merge match gene names and Eigengene/module/colorlabels
7.9 years ago yifangt ▴ 20
0
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3
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3.5k
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WGCNA error on block number related.
WGCNA block size subscript out of bounds
8.0 years ago yifangt ▴ 20
1
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6
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3.2k
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WGCNA with distance matrix only from newick data.
WGCNA eigengene hub genes
8.0 years ago yifangt ▴ 20
5
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6
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8.4k
views
WGCNA - module membership via max kME?
wgcna modules
updated 8.0 years ago by ★ 3.0k • written 8.1 years ago by ▴ 10
1
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1
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1.8k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 8.1 years ago by ▴ 760 • written 8.1 years ago by ▴ 40
2
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4
replies
2.7k
views
How to get an output from DESeq2 to be used in WGCNA package
deseq2 wgcna
updated 8.1 years ago by ★ 3.0k • written 8.1 years ago by • 0
0
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1
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1.7k
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WGNA export to external software
WGCNA network visualization external software cytoscape
updated 8.1 years ago by ★ 3.0k • written 8.1 years ago by • 0
0
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6
replies
1.9k
views
RNseq data for WGCNA
WGCNA
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 50
2
votes
2
replies
2.6k
views
WGCNA connecting trait data
WGCNA wgcna rownames
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by • 0
0
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1
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1.6k
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Meta-analysis with WGCNA
WGCNA
updated 8.2 years ago by ▴ 760 • written 8.2 years ago by ▴ 50
0
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4
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2.6k
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Problem with WGCNA - Module-trait relationship
wgcna
updated 8.2 years ago by ▴ 760 • written 8.2 years ago by ▴ 10
0
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1
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2.1k
views
WGCNA works on time course data
WGCNA
updated 8.2 years ago by ★ 3.0k • written 8.3 years ago by ▴ 50
2
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2
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2.2k
views
WGCNA - module membership preservation for low count genes
wgcna
8.3 years ago ly.leifels ▴ 10
0
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2
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1.8k
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WGCNA: Exporting MEs with Subject/Sample Identification
WGCNA
8.4 years ago Tox_scientist20 • 0
0
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0
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1.5k
views
Problem about functional annotation network of WGCNA modules (modified)
wgcna network analysis pathway analysis
8.4 years ago panagiotis.mokos ▴ 40
0
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3
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2.9k
views
failed to use multiple threads in R via openblas
wgcna R openblas blas threads
updated 8.4 years ago by 25k • written 8.4 years ago by • 0
0
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1
reply
2.3k
views
signed kME(MM) for finding hub genes in modules of interest
wgcna
8.4 years ago chiayi • 0
0
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2
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1.7k
views
WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped'
wgcna
updated 8.4 years ago by ★ 3.0k • written 8.4 years ago by • 0
0
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2
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1.8k
views
Normalization for comparative transcriptomics between species
deseq2 wgcna
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
4
votes
1
reply
2.4k
views
WGCNA always requires trait data?
wgcna rnaseq
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 20
0
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2
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2.0k
views
Intramodular connectivity RNA-seq WGCNA
wgcna
updated 8.5 years ago by ★ 3.0k • written 8.5 years ago by ▴ 20
0
votes
1
reply
1.4k
views
The cor and corp values in verboseScatterplot don't match with cor, corPvalueStudent results
WGCNA wgcna
updated 8.5 years ago by ▴ 760 • written 8.5 years ago by ▴ 50
1
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1
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1.3k
views
Can I apply WGCNA on unmatched time point microarray data and clinical data?
WGCNA
8.5 years ago joseph ▴ 50
335 results • Page 5 of 7
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Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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