Showing : wgcna • reset
3
votes
4
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7.8k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.1 years ago by ▴ 80
1
vote
1
reply
113
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 19 days ago by 52k • written 19 days ago by ▴ 10
0
votes
5
replies
685
views
WGCNA
WGCNA Normalization RNASeq
written 6 months ago by • 0
6
votes
8
replies
5.3k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.4 years ago by ▴ 60
0
votes
2
replies
5.0k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 6 weeks ago by • 0 • written 2.4 years ago by • 0
0
votes
1
reply
814
views
WGCNA
WGCNA DESeq2
updated 4 months ago by ★ 4.9k • written 4 months ago by • 0
0
votes
2
replies
453
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 7 weeks ago by • 0 • written 5 months ago by • 0
11
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6
replies
4.6k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 6 months ago by • 0 • written 9.0 years ago by ▴ 60
0
votes
1
reply
680
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 6 months ago by ★ 4.9k • written 6 months ago by • 0
0
votes
1
reply
392
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
0
votes
2
replies
422
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
7 months ago Vinesh • 0
0
votes
1
reply
259
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 7 months ago by ★ 4.9k • written 7 months ago by • 0
0
votes
1
reply
540
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 9 months ago by ★ 4.9k • written 9 months ago by • 0
0
votes
0
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365
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WGCNA module preservation using only adjacency matrix
WGCNA
9 months ago yang1641 • 0
3
votes
4
replies
1.4k
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
10 months ago sukeshinik5 ▴ 20
1
vote
1
reply
794
views
WGCNA
DEGselection RNASeqData WGCNA
updated 10 months ago by ▴ 760 • written 10 months ago by • 0
0
votes
0
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541
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
11 months ago Fernanda • 0
0
votes
1
reply
569
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 11 months ago by ▴ 760 • written 11 months ago by • 0
0
votes
1
reply
596
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 11 months ago by 68k • written 11 months ago by • 0
1
vote
3
replies
4.3k
views
WGNCA kME vs. kIM
WGCNA
updated 15 months ago by • 0 • written 10.0 years ago by ▴ 30
0
votes
0
replies
462
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
15 months ago k200987 • 0
0
votes
2
replies
788
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
17 months ago Gimena • 0
0
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2
replies
871
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
17 months ago w.cookson • 0
0
votes
1
reply
636
views
problem with ClusterRepro function
WGCNA
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
1
reply
1.3k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 19 months ago by ★ 4.9k • written 19 months ago by • 0
0
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2
replies
1.6k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 21 months ago by • 0
4
votes
3
replies
2.9k
views
WGCNA documentation not available
WGCNA
written 21 months ago by ▴ 10
0
votes
2
replies
2.4k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 15 months ago by • 0 • written 2.8 years ago by • 0
0
votes
1
reply
1.5k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 21 months ago by • 0 • written 3.7 years ago by • 0
1
vote
2
replies
1.7k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
21 months ago • updated 20 months ago Levi • 0
0
votes
2
replies
725
views
WGCNA less samples
RNA-Seq WGCNA Worms
21 months ago davca • 0
0
votes
1
reply
960
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 21 months ago by ★ 4.9k • written 21 months ago by • 0
1
vote
2
replies
1.2k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 22 months ago by ▴ 10
0
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1
reply
783
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.0 years ago by ★ 4.9k • written 2.0 years ago by • 0
0
votes
1
reply
5.0k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
1
reply
875
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by • 0
0
votes
1
reply
1.3k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by ▴ 20
2
votes
5
replies
2.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 16 months ago by • 0 • written 2.2 years ago by • 0
3
votes
6
replies
1.4k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.3 years ago by 52k • written 2.3 years ago by ▴ 10
1
vote
0
replies
963
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.2 years ago by 43k • written 2.3 years ago by ▴ 20
2
votes
1
reply
1.0k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 2.3 years ago by ▴ 50 • written 2.3 years ago by ▴ 10
0
votes
0
replies
761
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.3 years ago Levi • 0
3
votes
7
replies
2.3k
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
2.3 years ago Ortega-C ▴ 10
0
votes
1
reply
838
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.3 years ago by ★ 4.9k • written 2.3 years ago by • 0
0
votes
0
replies
913
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
2.4 years ago • updated 2.3 years ago Ortega-C ▴ 10
0
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2
replies
1.0k
views
WGCNA problem
WGCNA
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by • 0
0
votes
0
replies
909
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.4 years ago Levi • 0
0
votes
0
replies
760
views
Module Trait Corelation
WGCNA
2.4 years ago allanokwaro • 0
2
votes
3
replies
1.7k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.4 years ago by ★ 4.9k • written 2.5 years ago by ▴ 20
0
votes
0
replies
845
views
How to draw module significance barplot?
module_significance barplot WGCNA
2.5 years ago Sooni ▴ 10
335 results • Page 1 of 7
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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