Showing : WGCNA • reset
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WGCNA
WGCNA Normalization RNASeq
updated 1 day ago by • 0 • written 2 days ago by • 0
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284
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 10 days ago by ★ 4.7k • written 18 days ago by • 0
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174
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 28 days ago by ★ 4.7k • written 4 weeks ago by • 0
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2
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177
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
4 weeks ago • updated 28 days ago Vinesh • 0
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123
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Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 28 days ago by ★ 4.7k • written 29 days ago by • 0
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250
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
updated 10 days ago by • 0 • written 4.9 years ago by ▴ 60
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187
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WGCNA module preservation using only adjacency matrix
WGCNA
3 months ago yang1641 • 0
3
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4
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696
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What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
4 months ago sukeshinik5 ▴ 20
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493
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WGCNA
DEGselection RNASeqData WGCNA
updated 4 months ago by ▴ 760 • written 4 months ago by • 0
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291
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
5 months ago Fernanda • 0
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378
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 5 months ago by ▴ 760 • written 5 months ago by • 0
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396
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Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 5 months ago by 68k • written 5 months ago by • 0
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6
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2.9k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 22 months ago by • 0
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3.7k
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WGNCA kME vs. kIM
WGCNA
updated 9 months ago by • 0 • written 9.4 years ago by ▴ 30
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317
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query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
9 months ago k200987 • 0
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564
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
10 months ago Gimena • 0
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2
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627
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WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
11 months ago • updated 10 months ago w.cookson • 0
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478
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problem with ClusterRepro function
WGCNA
updated 11 months ago by 68k • written 11 months ago by • 0
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1
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941
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WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 12 months ago by ★ 4.7k • written 12 months ago by • 0
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1.3k
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Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 14 months ago by • 0
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2.3k
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WGCNA documentation not available
WGCNA
written 14 months ago by ▴ 10
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1.8k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 9 months ago by • 0 • written 2.2 years ago by • 0
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1.3k
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WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 14 months ago by • 0 • written 3.2 years ago by • 0
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1.3k
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Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
15 months ago • updated 14 months ago Levi • 0
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570
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WGCNA less samples
RNA-Seq WGCNA Worms
15 months ago davca • 0
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813
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WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 15 months ago by ★ 4.7k • written 15 months ago by • 0
1
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1
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777
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How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 16 months ago by ▴ 200 • written 16 months ago by ▴ 10
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644
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TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 18 months ago by ★ 4.7k • written 18 months ago by • 0
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4.7k
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Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
1
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745
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WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 20 months ago by ★ 4.7k • written 20 months ago by • 0
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1.1k
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Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 20 months ago by ★ 4.7k • written 20 months ago by ▴ 20
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1.8k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 10 months ago by • 0 • written 20 months ago by • 0
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1.2k
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 21 months ago by 52k • written 21 months ago by ▴ 10
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792
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 20 months ago by 43k • written 21 months ago by ▴ 20
2
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881
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WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 21 months ago by ▴ 50 • written 21 months ago by ▴ 10
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625
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blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
21 months ago Levi • 0
3
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7
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1.9k
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"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
21 months ago Ortega-C ▴ 10
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734
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WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 22 months ago by ★ 4.7k • written 22 months ago by • 0
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770
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Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
22 months ago Ortega-C ▴ 10
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869
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WGCNA problem
WGCNA
updated 22 months ago by ▴ 10 • written 22 months ago by • 0
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780
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
22 months ago Levi • 0
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655
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Module Trait Corelation
WGCNA
23 months ago allanokwaro • 0
2
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3
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1.4k
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Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 23 months ago by ★ 4.7k • written 23 months ago by ▴ 20
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718
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How to draw module significance barplot?
module_significance barplot WGCNA
2.0 years ago Sooni ▴ 10
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710
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Multiple way network preservation
wgcna
2.0 years ago madzayasodara • 0
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783
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WGCNA TOM file empty
WGCNA TOM
2.0 years ago gianni.drm • 0
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1.2k
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WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
2.0 years ago gianni.drm • 0
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1
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1.4k
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WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 11 months ago by ▴ 740 • written 2.0 years ago by • 0
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714
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In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 2.1 years ago by ▴ 50 • written 2.1 years ago by • 0
50 results • Page 1 of 1
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Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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