Showing : WGCNA • reset
1
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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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663
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Issue with Soft-Thresholding in WGCNA
WGCNA
written 8 months ago by • 0
3
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4
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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
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5
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895
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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
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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
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905
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WGCNA
WGCNA DESeq2
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
11
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6
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4.8k
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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
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763
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
reply
582
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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540
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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
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343
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
0
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1
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709
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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
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459
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WGCNA module preservation using only adjacency matrix
WGCNA
13 months ago yang1641 • 0
3
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4
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1.5k
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
14 months ago sukeshinik5 ▴ 20
1
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1
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985
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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608
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
14 months ago Fernanda • 0
0
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1
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631
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 15 months ago by ▴ 760 • written 15 months ago by • 0
0
votes
1
reply
662
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 15 months ago by 68k • written 15 months ago by • 0
1
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3
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4.5k
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WGNCA kME vs. kIM
WGCNA
updated 18 months ago by • 0 • written 10.2 years ago by ▴ 30
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0
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533
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
19 months ago k200987 • 0
0
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2
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890
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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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971
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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
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699
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problem with ClusterRepro function
WGCNA
updated 21 months ago by 68k • written 21 months ago by • 0
0
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1
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1.3k
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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
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 2.0 years ago by • 0
4
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3
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3.1k
views
WGCNA documentation not available
WGCNA
written 2.0 years ago by ▴ 10
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2
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2.5k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 19 months ago by • 0 • written 3.0 years ago by • 0
0
votes
1
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1.6k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 2.0 years ago by • 0 • written 4.0 years ago by • 0
1
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2
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1.9k
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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812
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WGCNA less samples
RNA-Seq WGCNA Worms
2.0 years ago davca • 0
0
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1
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1.0k
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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
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2
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1.3k
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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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850
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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
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1
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955
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
1
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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
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5
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2.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 20 months ago by • 0 • written 2.5 years ago by • 0
3
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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
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0
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1.0k
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 20
2
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1
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1.1k
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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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811
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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
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1
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909
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
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0
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975
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
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WGCNA problem
WGCNA
updated 2.6 years ago by ▴ 10 • written 2.6 years ago by • 0
0
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0
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975
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.7 years ago Levi • 0
0
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0
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807
views
Module Trait Corelation
WGCNA
2.7 years ago allanokwaro • 0
2
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3
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1.8k
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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
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0
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906
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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: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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…
Votes
C: DESeq2 Following RSEM
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
Awards • All
Popular Question to James W. MacDonald 68k
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Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
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