Showing : wgcna • reset
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1.9k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 14 months ago by • 0
1
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3
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2.9k
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WGNCA kME vs. kIM
WGCNA
updated 24 days ago by • 0 • written 8.7 years ago by ▴ 30
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92
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
4 weeks ago k200987 • 0
0
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2
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248
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
10 weeks ago Gimena • 0
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2
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272
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
11 weeks ago • updated 10 weeks ago w.cookson • 0
0
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1
reply
218
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problem with ClusterRepro function
WGCNA
updated 3 months ago by 66k • written 3 months ago by • 0
0
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1
reply
379
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 4 months ago by ★ 4.2k • written 4 months ago by • 0
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2
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620
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 6 months ago by • 0
4
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3
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1.2k
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WGCNA documentation not available
WGCNA
written 6 months ago by ▴ 10
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2
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1.0k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 weeks ago by • 0 • written 18 months ago by • 0
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1
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1.0k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 6 months ago by • 0 • written 2.5 years ago by • 0
1
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2
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766
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
6 months ago • updated 5 months ago Levi • 0
0
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2
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370
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WGCNA less samples
RNA-Seq WGCNA Worms
6 months ago davca • 0
0
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1
reply
565
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 7 months ago by ★ 4.2k • written 7 months ago by • 0
1
vote
1
reply
456
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 7 months ago by ▴ 190 • written 7 months ago by ▴ 10
0
votes
1
reply
426
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 9 months ago by ★ 4.2k • written 9 months ago by • 0
0
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1
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2.5k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 10 months ago by 66k • written 10 months ago by • 0
1
vote
1
reply
526
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 11 months ago by ★ 4.2k • written 11 months ago by • 0
0
votes
1
reply
686
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 12 months ago by ★ 4.2k • written 12 months ago by ▴ 20
2
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5
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1.3k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 weeks ago by • 0 • written 12 months ago by • 0
3
votes
6
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904
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 12 months ago by 51k • written 12 months ago by ▴ 10
1
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0
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533
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 12 months ago by 42k • written 12 months ago by ▴ 20
2
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1
reply
564
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 12 months ago by ▴ 50 • written 12 months ago by ▴ 10
0
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0
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462
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
12 months ago Levi • 0
3
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7
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1.3k
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
13 months ago Ortega-C ▴ 10
0
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1
reply
550
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 13 months ago by ★ 4.2k • written 13 months ago by • 0
0
votes
0
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578
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
13 months ago Ortega-C ▴ 10
0
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2
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646
views
WGCNA problem
WGCNA
updated 13 months ago by ▴ 10 • written 14 months ago by • 0
0
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0
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597
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
14 months ago Levi • 0
0
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0
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479
views
Module Trait Corelation
WGCNA
15 months ago allanokwaro • 0
2
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3
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985
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 14 months ago by ★ 4.2k • written 15 months ago by ▴ 20
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0
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482
views
How to draw module significance barplot?
module_significance barplot WGCNA
16 months ago Sooni ▴ 10
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0
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507
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Multiple way network preservation
wgcna
16 months ago madzayasodara • 0
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0
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571
views
WGCNA TOM file empty
WGCNA TOM
16 months ago gianni.drm • 0
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0
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901
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
16 months ago gianni.drm • 0
0
votes
1
reply
935
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 3 months ago by ▴ 740 • written 16 months ago by • 0
0
votes
1
reply
554
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 16 months ago by ▴ 50 • written 16 months ago by • 0
0
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0
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650
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
16 months ago S • 0
0
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0
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659
views
Problems running WGCNA
WGCNA
18 months ago S • 0
0
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0
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556
views
coexpression networks
WGCNA igraph
18 months ago María José • 0
0
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0
replies
561
views
A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
18 months ago Abdullah • 0
0
votes
0
replies
842
views
WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
19 months ago • updated 18 months ago bioinformaticssrm2011 • 0
2
votes
1
reply
835
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 21 months ago by ▴ 50 • written 21 months ago by ▴ 10
0
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1
reply
868
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 21 months ago by ▴ 50 • written 21 months ago by ▴ 20
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0
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593
views
MM-GS plot doesn't show any negative correlation
wgcna
22 months ago shubhankar.pawar • 0
0
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1
reply
1.1k
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 23 months ago by • 0 • written 23 months ago by • 0
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0
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658
views
ARACNe Sample Size
grndata GRN ARACNE WGCNA
23 months ago Harrsha • 0
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0
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540
views
Enrichment in genomic regions
Enrichment clusterPro WGCNA
23 months ago María José • 0
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0
replies
635
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference SampledBlockWiseModules WGCNA
23 months ago as8020 • 0
0
votes
0
replies
446
views
WGCNA consensusMEDdissimilrity
WGCNA
2.1 years ago María José • 0
50 results • Page 1 of 1
Recent ...
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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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Popular Question to Jonathan ▴ 10
Popular Question to Frederico Moraes Ferreira ▴ 100
Popular Question to richardallenfriedmanbrooklyn ▴ 20
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