Showing : WGCNA • reset
4
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3
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821
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WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
5
votes
8
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3.9k
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Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
0
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2
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470
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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
1
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2
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2.6k
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WGNCA kME vs. kIM
WGCNA
updated 11 months ago by • 0 • written 8.6 years ago by ▴ 30
0
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5
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1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
11
votes
4
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7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 22 days ago by ★ 3.0k • written 9.1 years ago by ▴ 150
0
votes
2
replies
204
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
21 days ago • updated 16 days ago w.cookson • 0
0
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2
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161
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
15 days ago Gimena • 0
6
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6
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2.6k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
0
votes
1
reply
470
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by ★ 4.0k • written 5 months ago by • 0
0
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1
reply
978
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 4 months ago by • 0 • written 2.4 years ago by • 0
2
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5
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1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 1 day ago by • 0 • written 10 months ago by • 0
3
votes
7
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1.1k
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
11 months ago Ortega-C ▴ 10
0
votes
1
reply
1.8k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
1
reply
578
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 20
0
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2
replies
295
views
WGCNA less samples
RNA-Seq WGCNA Worms
4 months ago davca • 0
0
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1
reply
851
views
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
1
vote
1
reply
476
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 9 months ago by ★ 4.0k • written 9 months ago by • 0
3
votes
6
replies
813
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 10 months ago by ▴ 10
0
votes
1
reply
372
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
0
votes
1
reply
155
views
problem with ClusterRepro function
WGCNA
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
votes
2
replies
586
views
WGCNA problem
WGCNA
updated 11 months ago by ▴ 10 • written 12 months ago by • 0
1
vote
1
reply
377
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 5 months ago by ▴ 190 • written 5 months ago by ▴ 10
0
votes
0
replies
528
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
12 months ago • updated 11 months ago Ortega-C ▴ 10
1
vote
2
replies
637
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
4 months ago • updated 3 months ago Levi • 0
1
vote
0
replies
452
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 10 months ago by ▴ 20
0
votes
1
reply
857
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 6 weeks ago by ▴ 720 • written 14 months ago by • 0
0
votes
1
reply
513
views
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
0
votes
1
reply
231
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 10 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
0
votes
2
replies
790
views
Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA Module Detection
updated 3 months ago by • 0 • written 4.5 years ago by • 0
0
votes
0
replies
406
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
11 months ago Levi • 0
0
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1
reply
1.0k
views
WGCNA Preservation error
preservation WGCNA
updated 12 weeks ago by • 0 • written 2.3 years ago by • 0
0
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2
replies
1.3k
views
WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna WGCNA
written 2.1 years ago by • 0
2
votes
1
reply
486
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 10 months ago by ▴ 50 • written 10 months ago by ▴ 10
34 results • Page 1 of 1
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Replies
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by sredemption • 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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