Showing : wgcna • reset
3
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4
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7.9k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.1 years ago by ▴ 80
1
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1
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159
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 7 weeks ago by 53k • written 7 weeks ago by ▴ 10
0
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5
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710
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WGCNA
WGCNA Normalization RNASeq
written 7 months ago by • 0
6
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8
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5.4k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.5 years ago by ▴ 60
0
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2
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5.1k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 11 weeks ago by • 0 • written 2.5 years ago by • 0
0
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1
reply
846
views
WGCNA
WGCNA DESeq2
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
0
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2
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481
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Issue with Soft-Thresholding in WGCNA
WGCNA
written 6 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 7 months ago by • 0 • written 9.1 years ago by ▴ 60
0
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1
reply
708
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 7 months ago by ★ 4.9k • written 8 months ago by • 0
0
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1
reply
424
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 8 months ago by ★ 4.9k • written 8 months ago by • 0
0
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2
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453
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
8 months ago Vinesh • 0
0
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1
reply
289
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 8 months ago by ★ 4.9k • written 8 months ago by • 0
0
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1
reply
578
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
0
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0
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384
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WGCNA module preservation using only adjacency matrix
WGCNA
10 months ago yang1641 • 0
3
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4
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1.4k
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
11 months ago sukeshinik5 ▴ 20
1
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1
reply
823
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WGCNA
DEGselection RNASeqData WGCNA
updated 11 months ago by ▴ 760 • written 11 months ago by • 0
0
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0
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561
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
12 months ago Fernanda • 0
0
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1
reply
594
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 12 months ago by ▴ 760 • written 12 months ago by • 0
0
votes
1
reply
623
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 12 months ago by 68k • written 12 months ago by • 0
1
vote
3
replies
4.3k
views
WGNCA kME vs. kIM
WGCNA
updated 16 months ago by • 0 • written 10.0 years ago by ▴ 30
0
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0
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478
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
16 months ago k200987 • 0
0
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2
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816
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
18 months ago Gimena • 0
0
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2
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897
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
18 months ago w.cookson • 0
0
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1
reply
655
views
problem with ClusterRepro function
WGCNA
updated 18 months ago by 68k • written 18 months ago by • 0
0
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1
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1.3k
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 20 months ago by ★ 4.9k • written 20 months ago by • 0
0
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2
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1.6k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 22 months ago by • 0
4
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3
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3.0k
views
WGCNA documentation not available
WGCNA
written 22 months ago by ▴ 10
0
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2
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2.4k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 16 months ago by • 0 • written 2.9 years ago by • 0
0
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1
reply
1.5k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 22 months ago by • 0 • written 3.8 years ago by • 0
1
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2
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1.7k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
22 months ago • updated 21 months ago Levi • 0
0
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2
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754
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WGCNA less samples
RNA-Seq WGCNA Worms
22 months ago davca • 0
0
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1
reply
992
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 22 months ago by ★ 4.9k • written 23 months ago by • 0
1
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2
replies
1.2k
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
written 23 months ago by ▴ 10
0
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1
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801
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 2.1 years ago by ★ 4.9k • written 2.1 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 2.2 years ago by 68k • written 2.2 years ago by • 0
1
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1
reply
896
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 2.3 years ago by ★ 4.9k • written 2.3 years ago by • 0
0
votes
1
reply
1.4k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 2.3 years ago by ★ 4.9k • written 2.3 years ago by ▴ 20
2
votes
5
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2.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 17 months ago by • 0 • written 2.3 years ago by • 0
3
votes
6
replies
1.5k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
1
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0
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981
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 2.3 years ago by 43k • written 2.4 years ago by ▴ 20
2
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1
reply
1.1k
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 2.4 years ago by ▴ 10
0
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0
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781
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
2.4 years ago Levi • 0
3
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7
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2.4k
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
2.4 years ago Ortega-C ▴ 10
0
votes
1
reply
859
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 2.4 years ago by ★ 4.9k • written 2.4 years ago by • 0
0
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0
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933
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
2.4 years ago Ortega-C ▴ 10
0
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2
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1.1k
views
WGCNA problem
WGCNA
updated 2.4 years ago by ▴ 10 • written 2.5 years ago by • 0
0
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0
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929
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
2.5 years ago Levi • 0
0
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0
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770
views
Module Trait Corelation
WGCNA
2.5 years ago allanokwaro • 0
2
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3
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1.7k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.5 years ago by ★ 4.9k • written 2.6 years ago by ▴ 20
0
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0
replies
859
views
How to draw module significance barplot?
module_significance barplot WGCNA
2.6 years ago Sooni ▴ 10
335 results • Page 1 of 7
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Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Answer: Help with defining groups by Gordon Smyth 53k
Defining sample groups is separate to reading in the DIA-NN data, because the sample conditions and covariates are not necessarily coded in…
Comment: Sharing a collection of datasets in ExperimentHub by Peter Hickey ▴ 760
The [**scRNAseq**](https://bioconductor.org/packages/scRNAseq/) package ([source on GitHub](https://github.com/LTLA/scRNAseq)) might serve …
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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