Showing : WGCNA • reset
1
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315
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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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639
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Issue with Soft-Thresholding in WGCNA
WGCNA
written 7 months ago by • 0
3
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4
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8.0k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.3 years ago by ▴ 80
0
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5
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871
views
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 2.6 years ago by • 0
0
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1
reply
892
views
WGCNA
WGCNA DESeq2
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
11
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6
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4.7k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 8 months ago by • 0 • written 9.2 years ago by ▴ 60
0
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1
reply
747
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
votes
1
reply
560
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 9 months ago by ★ 5.0k • written 10 months ago by • 0
0
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2
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522
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
10 months ago • updated 9 months ago Vinesh • 0
0
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1
reply
332
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
votes
1
reply
674
views
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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437
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WGCNA module preservation using only adjacency matrix
WGCNA
12 months ago yang1641 • 0
3
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4
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1.5k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
13 months ago sukeshinik5 ▴ 20
1
vote
1
reply
964
views
WGCNA
DEGselection RNASeqData WGCNA
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
0
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0
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591
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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
reply
621
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
0
votes
1
reply
651
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
3
replies
4.4k
views
WGNCA kME vs. kIM
WGCNA
updated 18 months ago by • 0 • written 10.2 years ago by ▴ 30
0
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0
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521
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
18 months ago k200987 • 0
0
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2
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865
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
19 months ago Gimena • 0
0
votes
2
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953
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
20 months ago • updated 19 months ago w.cookson • 0
0
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1
reply
686
views
problem with ClusterRepro function
WGCNA
updated 20 months ago by 68k • written 20 months ago by • 0
0
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1
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1.3k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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2
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1.7k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 23 months ago by • 0
4
votes
3
replies
3.0k
views
WGCNA documentation not available
WGCNA
written 23 months ago by ▴ 10
0
votes
2
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2.5k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 18 months ago by • 0 • written 3.0 years ago by • 0
0
votes
1
reply
1.6k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 23 months ago by • 0 • written 3.9 years ago by • 0
1
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2
replies
1.8k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
24 months ago • updated 23 months ago Levi • 0
0
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2
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792
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WGCNA less samples
RNA-Seq WGCNA Worms
24 months ago davca • 0
0
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1
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1.0k
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
1
vote
2
replies
1.3k
views
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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837
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.2 years ago by ★ 5.0k • written 2.2 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 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
1
reply
941
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
1.4k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 2.4 years ago by ★ 5.0k • written 2.4 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 19 months ago by • 0 • written 2.4 years ago by • 0
3
votes
6
replies
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
replies
1.0k
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.5 years ago by 43k • written 2.5 years ago by ▴ 20
2
votes
1
reply
1.1k
views
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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803
views
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
2.5 years ago Ortega-C ▴ 10
0
votes
1
reply
895
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.5 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
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0
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964
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
views
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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961
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.6 years ago Levi • 0
0
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0
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799
views
Module Trait Corelation
WGCNA
2.7 years ago allanokwaro • 0
2
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3
replies
1.8k
views
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
votes
0
replies
893
views
How to draw module significance barplot?
module_significance barplot WGCNA
2.7 years ago Sooni ▴ 10
335 results • Page 1 of 7
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Replies
Answer: Alternative to BrainArray custom CDF packages for Affymetrix chips? by Guido Hooiveld ★ 4.1k
It seems that through the Internet Archive these files can be obtained: https://web.archive.org/web/20240710102334/http://brainarray.mbn…
Comment: Getting a large intercept with DESeq2 by Denise • 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Answer: Error installing Seqinfo by fabio.marroni • 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
Votes
Comment: Error installing Seqinfo
Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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