Showing : WGCNA • reset
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Issue with Soft-Thresholding in WGCNA
WGCNA
15 hours ago Μαρία • 0
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 5 weeks ago by • 0 • written 8.6 years ago by ▴ 60
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2
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361
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WGCNA
WGCNA Normalization RNASeq
updated 5 weeks ago by • 0 • written 6 weeks ago by • 0
0
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1
reply
390
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In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowick TomType
WGCNA pickSoftThreshold SignedNowick
updated 7 weeks ago by ★ 4.8k • written 8 weeks ago by • 0
0
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1
reply
226
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 9 weeks ago by ★ 4.8k • written 10 weeks ago by • 0
0
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2
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236
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
10 weeks ago • updated 9 weeks ago Vinesh • 0
0
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1
reply
147
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Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 9 weeks ago by ★ 4.8k • written 9 weeks ago by • 0
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1
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330
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 4 months ago by ★ 4.8k • written 4 months ago by • 0
6
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7
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4.7k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.0 years ago by ▴ 60
0
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0
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228
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WGCNA module preservation using only adjacency matrix
WGCNA
4 months ago yang1641 • 0
3
votes
4
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933
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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
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1
reply
575
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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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340
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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
419
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WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 6 months ago by ▴ 760 • written 6 months ago by • 0
0
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1
reply
441
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 6 months ago by 68k • written 6 months ago by • 0
0
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6
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3.1k
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blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 24 months ago by • 0
1
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3
replies
3.9k
views
WGNCA kME vs. kIM
WGCNA
updated 10 months ago by • 0 • written 9.5 years ago by ▴ 30
0
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0
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348
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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
replies
617
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
12 months ago Gimena • 0
0
votes
2
replies
671
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
12 months ago w.cookson • 0
0
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1
reply
522
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problem with ClusterRepro function
WGCNA
updated 12 months ago by 68k • written 12 months ago by • 0
0
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1
reply
1.0k
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 13 months ago by ★ 4.8k • written 13 months ago by • 0
0
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2
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1.4k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 16 months ago by • 0
4
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3
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2.5k
views
WGCNA documentation not available
WGCNA
written 16 months ago by ▴ 10
0
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2
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2.0k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 10 months ago by • 0 • written 2.4 years ago by • 0
0
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1
reply
1.4k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 16 months ago by • 0 • written 3.3 years ago by • 0
1
vote
2
replies
1.5k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
16 months ago • updated 15 months ago Levi • 0
0
votes
2
replies
592
views
WGCNA less samples
RNA-Seq WGCNA Worms
16 months ago davca • 0
0
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1
reply
844
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 16 months ago by ★ 4.8k • written 16 months ago by • 0
1
vote
1
reply
830
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
682
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 19 months ago by ★ 4.8k • 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
773
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 21 months ago by ★ 4.8k • written 21 months ago by • 0
0
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1
reply
1.2k
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 21 months ago by ★ 4.8k • 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
votes
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
833
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 22 months ago by 43k • written 22 months ago by ▴ 20
2
votes
1
reply
923
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
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0
replies
659
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
759
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 23 months ago by ★ 4.8k • written 23 months ago by • 0
0
votes
0
replies
791
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
23 months ago Ortega-C ▴ 10
0
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2
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903
views
WGCNA problem
WGCNA
updated 23 months ago by ▴ 10 • written 23 months ago by • 0
0
votes
0
replies
800
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
24 months ago Levi • 0
0
votes
0
replies
677
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 ★ 4.8k • written 2.1 years ago by ▴ 20
0
votes
0
replies
746
views
How to draw module significance barplot?
module_significance barplot WGCNA
2.1 years ago Sooni ▴ 10
0
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0
replies
736
views
Multiple way network preservation
wgcna
2.1 years ago madzayasodara • 0
0
votes
0
replies
809
views
WGCNA TOM file empty
WGCNA TOM
2.1 years ago gianni.drm • 0
0
votes
0
replies
1.3k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
2.2 years ago gianni.drm • 0
50 results • Page 1 of 1
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Answer: compute_fasta_digest does not match Salmon index hash by Michael Love 43k
Can you provide more details on when this is happening? The salmon index is the definitive hash associated with the quant files, so I'm con…
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
Oh wait. You want to map from Ensembl to NCBI? That's hard to do with model organisms, let alone non-model. This `OrgDb` doesn't have Ensem…
Answer: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species by James W. MacDonald 68k
You can use the `AnnotationHub` ``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% sna…
Answer: List of Deprecated Packages for Bioc3.20 by shepherl 4.1k
HTqPCR has been fixed and will be re-instated in 3.21
Comment: Question about using LRT test for time course experiments with DESeq2 by Rob • 0
Just to pick up on this thread as its really helpful for understanding the LRT test. The LRT test is given any genes that change within the…
Votes
what the test method for enrichGO in clusterProfiler?
A: single-cells RNA-seq analysis by MAST with unbalanced group size
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
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