Showing : wgcna • reset
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 28 days ago by ★ 4.6k • written 28 days ago by • 0
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6
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3.9k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.7 years ago by ▴ 60
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120
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WGCNA module preservation using only adjacency matrix
WGCNA
5 weeks ago yang1641 • 0
3
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4
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488
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
9 weeks ago sukeshinik5 ▴ 20
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341
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WGCNA
DEGselection RNASeqData WGCNA
updated 10 weeks ago by ▴ 760 • written 10 weeks ago by • 0
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210
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
3 months ago Fernanda • 0
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1
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302
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
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1
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311
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Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 3 months ago by 67k • written 3 months ago by • 0
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6
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2.7k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 20 months ago by • 0
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3
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3.5k
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WGNCA kME vs. kIM
WGCNA
updated 7 months ago by • 0 • written 9.3 years ago by ▴ 30
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262
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
7 months ago k200987 • 0
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2
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493
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
8 months ago Gimena • 0
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2
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561
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
8 months ago w.cookson • 0
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424
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problem with ClusterRepro function
WGCNA
updated 9 months ago by 67k • written 9 months ago by • 0
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816
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
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1.1k
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 12 months ago by • 0
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2.0k
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WGCNA documentation not available
WGCNA
written 12 months ago by ▴ 10
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1.6k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 7 months ago by • 0 • written 2.1 years ago by • 0
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1
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1.3k
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WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 12 months ago by • 0 • written 3.0 years ago by • 0
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2
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1.2k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
12 months ago Levi • 0
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2
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532
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WGCNA less samples
RNA-Seq WGCNA Worms
13 months ago davca • 0
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1
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762
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
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705
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 14 months ago by ▴ 200 • written 14 months ago by ▴ 10
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592
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TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
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4.4k
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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 17 months ago by 67k • written 17 months ago by • 0
1
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1
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700
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
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1
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969
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 18 months ago by ★ 4.6k • written 18 months ago by ▴ 20
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5
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1.7k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 months ago by • 0 • written 18 months ago by • 0
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6
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1.2k
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 18 months ago by 52k • written 19 months ago by ▴ 10
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735
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 18 months ago by 43k • written 19 months ago by ▴ 20
2
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1
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818
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 18 months ago by ▴ 50 • written 19 months ago by ▴ 10
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588
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
19 months ago Levi • 0
3
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7
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1.8k
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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
19 months ago Ortega-C ▴ 10
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693
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
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0
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729
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
20 months ago Ortega-C ▴ 10
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2
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820
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WGCNA problem
WGCNA
updated 20 months ago by ▴ 10 • written 20 months ago by • 0
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0
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740
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
20 months ago Levi • 0
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0
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611
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Module Trait Corelation
WGCNA
21 months ago allanokwaro • 0
2
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3
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1.3k
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 21 months ago by ★ 4.6k • written 21 months ago by ▴ 20
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655
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How to draw module significance barplot?
module_significance barplot WGCNA
22 months ago Sooni ▴ 10
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673
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Multiple way network preservation
wgcna
22 months ago madzayasodara • 0
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747
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WGCNA TOM file empty
WGCNA TOM
22 months ago gianni.drm • 0
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1.2k
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
22 months ago gianni.drm • 0
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1
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1.3k
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WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 9 months ago by ▴ 740 • written 22 months ago by • 0
0
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1
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672
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In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 23 months ago by ▴ 50 • written 23 months ago by • 0
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804
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
23 months ago S • 0
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0
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795
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Problems running WGCNA
WGCNA
2.0 years ago S • 0
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670
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coexpression networks
WGCNA igraph
2.1 years ago María José • 0
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725
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
2.1 years ago Abdullah • 0
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0
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1.1k
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WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.1 years ago • updated 12 weeks ago bioinformaticssrm2011 • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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