Showing : wgcna • reset
11
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6
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4.2k
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WGCNA with paired samples
wgcna paired samples exercise
updated 29 days ago by • 0 • written 8.6 years ago by ▴ 60
0
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2
replies
348
views
WGCNA
WGCNA Normalization RNASeq
updated 4 weeks ago by • 0 • written 4 weeks ago by • 0
0
votes
1
reply
373
views
In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 5 weeks ago by ★ 4.7k • written 6 weeks ago by • 0
0
votes
1
reply
216
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 8 weeks ago by ★ 4.7k • written 9 weeks ago by • 0
0
votes
2
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226
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
8 weeks ago Vinesh • 0
0
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1
reply
144
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 8 weeks ago by ★ 4.7k • written 8 weeks ago by • 0
0
votes
1
reply
307
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 4 months ago by ★ 4.7k • written 4 months ago by • 0
6
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7
replies
4.6k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.9 years ago by ▴ 60
0
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0
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223
views
WGCNA module preservation using only adjacency matrix
WGCNA
4 months ago yang1641 • 0
3
votes
4
replies
877
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
5 months ago sukeshinik5 ▴ 20
1
vote
1
reply
554
views
WGCNA
DEGselection RNASeqData WGCNA
updated 5 months ago by ▴ 760 • written 5 months ago by • 0
0
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0
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334
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
6 months ago Fernanda • 0
0
votes
1
reply
408
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 6 months ago by ▴ 760 • written 6 months ago by • 0
0
votes
1
reply
429
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 6 months ago by 68k • written 6 months ago by • 0
0
votes
6
replies
3.1k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 23 months ago by • 0
1
vote
3
replies
3.9k
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WGNCA kME vs. kIM
WGCNA
updated 10 months ago by • 0 • written 9.5 years ago by ▴ 30
0
votes
0
replies
342
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
10 months ago k200987 • 0
0
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2
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608
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
11 months ago Gimena • 0
0
votes
2
replies
657
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
12 months ago • updated 11 months ago w.cookson • 0
0
votes
1
reply
510
views
problem with ClusterRepro function
WGCNA
updated 12 months ago by 68k • written 12 months ago by • 0
0
votes
1
reply
1.0k
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 13 months ago by ★ 4.7k • written 13 months ago by • 0
0
votes
2
replies
1.3k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 15 months ago by • 0
4
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3
replies
2.4k
views
WGCNA documentation not available
WGCNA
written 15 months ago by ▴ 10
0
votes
2
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1.9k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 10 months ago by • 0 • written 2.3 years ago by • 0
0
votes
1
reply
1.4k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 15 months ago by • 0 • written 3.3 years ago by • 0
1
vote
2
replies
1.4k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
16 months ago • updated 15 months ago Levi • 0
0
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2
replies
590
views
WGCNA less samples
RNA-Seq WGCNA Worms
16 months ago davca • 0
0
votes
1
reply
838
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 16 months ago by ★ 4.7k • written 16 months ago by • 0
1
vote
1
reply
823
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 17 months ago by ▴ 200 • written 17 months ago by ▴ 10
0
votes
1
reply
674
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 19 months ago by ★ 4.7k • written 19 months ago by • 0
0
votes
1
reply
4.9k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 20 months ago by 68k • written 20 months ago by • 0
1
vote
1
reply
769
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 21 months ago by ★ 4.7k • written 21 months ago by • 0
0
votes
1
reply
1.1k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 21 months ago by ★ 4.7k • written 21 months ago by ▴ 20
2
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5
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1.9k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 11 months ago by • 0 • written 21 months ago by • 0
3
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6
replies
1.3k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 22 months ago by 52k • written 22 months ago by ▴ 10
1
vote
0
replies
827
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 21 months ago by 43k • written 22 months ago by ▴ 20
2
votes
1
reply
917
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 22 months ago by ▴ 50 • written 22 months ago by ▴ 10
0
votes
0
replies
651
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
22 months ago Levi • 0
3
votes
7
replies
2.0k
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
22 months ago Ortega-C ▴ 10
0
votes
1
reply
758
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 23 months ago by ★ 4.7k • written 23 months ago by • 0
0
votes
0
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787
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
23 months ago Ortega-C ▴ 10
0
votes
2
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895
views
WGCNA problem
WGCNA
updated 23 months ago by ▴ 10 • written 23 months ago by • 0
0
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0
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796
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
23 months ago Levi • 0
0
votes
0
replies
675
views
Module Trait Corelation
WGCNA
2.0 years ago allanokwaro • 0
2
votes
3
replies
1.4k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 2.0 years ago by ★ 4.7k • written 2.0 years ago by ▴ 20
0
votes
0
replies
740
views
How to draw module significance barplot?
module_significance barplot WGCNA
2.1 years ago Sooni ▴ 10
0
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0
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731
views
Multiple way network preservation
wgcna
2.1 years ago madzayasodara • 0
0
votes
0
replies
804
views
WGCNA TOM file empty
WGCNA TOM
2.1 years ago gianni.drm • 0
0
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0
replies
1.3k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
2.1 years ago gianni.drm • 0
0
votes
1
reply
1.4k
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 12 months ago by ▴ 740 • written 2.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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