Showing : wgcna • reset
1
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334
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 3 months ago by ▴ 10
0
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4
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655
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Issue with Soft-Thresholding in WGCNA
WGCNA
written 8 months ago by • 0
3
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4
replies
8.0k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.3 years ago by ▴ 80
0
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5
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887
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WGCNA
WGCNA Normalization RNASeq
written 9 months ago by • 0
6
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8
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5.6k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.6 years ago by ▴ 60
0
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2
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5.2k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 4 months ago by • 0 • written 2.7 years ago by • 0
0
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1
reply
900
views
WGCNA
WGCNA DESeq2
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
11
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6
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4.8k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 9 months ago by • 0 • written 9.3 years ago by ▴ 60
0
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1
reply
755
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 9 months ago by ★ 5.0k • written 10 months ago by • 0
0
votes
1
reply
578
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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2
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533
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
10 months ago Vinesh • 0
0
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1
reply
338
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
votes
1
reply
700
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 12 months ago by ★ 5.0k • written 12 months ago by • 0
0
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0
replies
450
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WGCNA module preservation using only adjacency matrix
WGCNA
12 months ago yang1641 • 0
3
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4
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1.5k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
13 months ago sukeshinik5 ▴ 20
1
vote
1
reply
981
views
WGCNA
DEGselection RNASeqData WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
0
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0
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600
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
14 months ago Fernanda • 0
0
votes
1
reply
628
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
0
votes
1
reply
657
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 14 months ago by 68k • written 15 months ago by • 0
1
vote
3
replies
4.4k
views
WGNCA kME vs. kIM
WGCNA
updated 18 months ago by • 0 • written 10.2 years ago by ▴ 30
0
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0
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528
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
18 months ago k200987 • 0
0
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2
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880
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
20 months ago Gimena • 0
0
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2
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964
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
20 months ago w.cookson • 0
0
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1
reply
694
views
problem with ClusterRepro function
WGCNA
updated 20 months ago by 68k • written 20 months ago by • 0
0
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1
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1.3k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
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2
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1.7k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 24 months ago by • 0
4
votes
3
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3.1k
views
WGCNA documentation not available
WGCNA
written 24 months ago by ▴ 10
0
votes
2
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2.5k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 18 months ago by • 0 • written 3.0 years ago by • 0
0
votes
1
reply
1.6k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 24 months ago by • 0 • written 4.0 years ago by • 0
1
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2
replies
1.8k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
2.0 years ago • updated 23 months ago Levi • 0
0
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2
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804
views
WGCNA less samples
RNA-Seq WGCNA Worms
2.0 years ago davca • 0
0
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1
reply
1.0k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
1
vote
2
replies
1.3k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 2.1 years ago by ▴ 10
0
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1
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844
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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1
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5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
vote
1
reply
951
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
1.4k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 20
2
votes
5
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2.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 19 months ago by • 0 • written 2.5 years ago by • 0
3
votes
6
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1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
1
vote
0
replies
1.0k
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 20
2
votes
1
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1.1k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 2.5 years ago by ▴ 50 • written 2.5 years ago by ▴ 10
0
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0
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810
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.5 years ago Levi • 0
3
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7
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2.5k
views
"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
2.6 years ago Ortega-C ▴ 10
0
votes
1
reply
902
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
votes
0
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971
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
2.6 years ago Ortega-C ▴ 10
0
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2
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1.1k
views
WGCNA problem
WGCNA
updated 2.6 years ago by ▴ 10 • written 2.6 years ago by • 0
0
votes
0
replies
970
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.7 years ago Levi • 0
0
votes
0
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803
views
Module Trait Corelation
WGCNA
2.7 years ago allanokwaro • 0
2
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3
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1.8k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 20
0
votes
0
replies
902
views
How to draw module significance barplot?
module_significance barplot WGCNA
2.8 years ago Sooni ▴ 10
335 results • Page 1 of 7
Recent ...
Replies
Comment: GOseq Probability Weight Function bad fit by ejasge.r.m • 0
When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
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Popular Question to James W. MacDonald 68k
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