Showing : WGCNA • reset
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
21 days ago Gimena • 0
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2
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212
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
27 days ago • updated 22 days ago w.cookson • 0
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1
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161
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problem with ClusterRepro function
WGCNA
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
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1
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243
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 10 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
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2
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484
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by • 0
4
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3
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857
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WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
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2
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648
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago Levi • 0
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2
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300
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
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1
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478
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
1
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1
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388
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by ▴ 190 • written 6 months ago by ▴ 10
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1
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379
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
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1
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1.8k
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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 9 months ago by 65k • written 9 months ago by • 0
1
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1
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481
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
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1
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591
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 20
2
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5
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1.1k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 7 days ago by • 0 • written 10 months ago by • 0
3
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6
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827
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 11 months ago by ▴ 10
1
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0
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459
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 11 months ago by ▴ 20
2
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1
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496
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 10 months ago by ▴ 50 • written 11 months ago by ▴ 10
0
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0
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415
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
3
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7
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1.2k
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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
11 months ago Ortega-C ▴ 10
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1
reply
516
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 11 months ago by ★ 4.0k • written 11 months ago by • 0
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0
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535
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
12 months ago Ortega-C ▴ 10
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2
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598
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WGCNA problem
WGCNA
updated 12 months ago by ▴ 10 • written 12 months ago by • 0
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5
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1.6k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
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0
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555
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
12 months ago Levi • 0
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0
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407
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Module Trait Corelation
WGCNA
13 months ago allanokwaro • 0
2
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3
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870
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 20
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0
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430
views
How to draw module significance barplot?
module_significance barplot WGCNA
14 months ago Sooni ▴ 10
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471
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Multiple way network preservation
wgcna
14 months ago madzayasodara • 0
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523
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WGCNA TOM file empty
WGCNA TOM
14 months ago gianni.drm • 0
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0
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801
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
14 months ago gianni.drm • 0
0
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1
reply
864
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 7 weeks ago by ▴ 720 • written 14 months ago by • 0
0
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1
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512
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 15 months ago by ▴ 50 • written 15 months ago by • 0
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0
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612
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago S • 0
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0
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586
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Problems running WGCNA
WGCNA
16 months ago S • 0
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0
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520
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coexpression networks
WGCNA igraph
17 months ago María José • 0
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0
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496
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A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
17 months ago Abdullah • 0
0
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1
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867
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 months ago by • 0 • written 17 months ago by • 0
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0
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731
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WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
17 months ago bioinformaticssrm2011 • 0
2
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1
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783
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WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 19 months ago by ▴ 50 • written 19 months ago by ▴ 10
0
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1
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805
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 20 months ago by ▴ 50 • written 20 months ago by ▴ 20
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0
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552
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MM-GS plot doesn't show any negative correlation
wgcna
21 months ago shubhankar.pawar • 0
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1
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940
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 21 months ago by • 0 • written 21 months ago by • 0
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0
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622
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ARACNe Sample Size
grndata GRN ARACNE WGCNA
21 months ago Harrsha • 0
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0
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512
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Enrichment in genomic regions
Enrichment clusterPro WGCNA
21 months ago María José • 0
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0
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604
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How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference SampledBlockWiseModules WGCNA
21 months ago as8020 • 0
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0
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415
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WGCNA consensusMEDdissimilrity
WGCNA
23 months ago María José • 0
1
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3
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1.7k
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WGCNA error
WGCNA
24 months ago • updated 23 months ago ayabalbaa1990 • 0
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747
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
24 months ago chiwut.wong • 0
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0
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648
views
FILTER GENES FOR WGCNA
WGCNA
24 months ago María José • 0
50 results • Page 1 of 1
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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…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
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?
Answer: How to retrieve gene ontology GO class from gene list?
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