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wgcna
•
reset
0
votes
0
replies
29
views
WGCNA sample-data preprocessing order
Microarray
WGCNA
GeneExpression
1 day ago
Reuben
• 0
0
votes
1
reply
191
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 8 weeks ago by
ATpoint
★ 4.6k • written 8 weeks ago by
siobhan.dietz
• 0
6
votes
6
replies
4.0k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.8 years ago by
Colari19
▴ 60
0
votes
0
replies
151
views
WGCNA module preservation using only adjacency matrix
WGCNA
9 weeks ago
yang1641
• 0
3
votes
4
replies
574
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
3 months ago
sukeshinik5
▴ 20
1
vote
1
reply
413
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 3 months ago by
Lluís Revilla Sancho
▴ 760 • written 3 months ago by
Nasim
• 0
0
votes
0
replies
243
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
4 months ago
Fernanda
• 0
0
votes
1
reply
329
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 4 months ago by
Lluís Revilla Sancho
▴ 760 • written 4 months ago by
emilymily77
• 0
0
votes
1
reply
345
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 4 months ago by
James W. MacDonald
67k • written 4 months ago by
bioinformaticssrm2011
• 0
0
votes
6
replies
2.8k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 21 months ago by
mauricio.microbiol
• 0
1
vote
3
replies
3.6k
views
WGNCA kME vs. kIM
WGCNA
updated 8 months ago by
Vitor
• 0 • written 9.3 years ago by
akridgerunner
▴ 30
0
votes
0
replies
284
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
8 months ago
k200987
• 0
0
votes
2
replies
529
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
9 months ago
Gimena
• 0
0
votes
2
replies
584
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
9 months ago
w.cookson
• 0
0
votes
1
reply
447
views
problem with ClusterRepro function
WGCNA
updated 10 months ago by
James W. MacDonald
67k • written 10 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
881
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 11 months ago by
ATpoint
★ 4.6k • written 11 months ago by
Priya
• 0
0
votes
2
replies
1.2k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 13 months ago by
aehall26
• 0
4
votes
3
replies
2.1k
views
WGCNA documentation not available
WGCNA
written 13 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
1.7k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 8 months ago by
mariakenneth147
• 0 • written 2.2 years ago by
pharamac
• 0
0
votes
1
reply
1.3k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 13 months ago by
Vanatta
• 0 • written 3.1 years ago by
mairah.khan
• 0
1
vote
2
replies
1.3k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
13 months ago
Levi
• 0
0
votes
2
replies
549
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
14 months ago
davca
• 0
0
votes
1
reply
780
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 14 months ago by
ATpoint
★ 4.6k • written 14 months ago by
ellen.francis
• 0
1
vote
1
reply
737
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 15 months ago by
tangming2005
▴ 200 • written 15 months ago by
meenae
▴ 10
0
votes
1
reply
610
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 17 months ago by
ATpoint
★ 4.6k • written 17 months ago by
jiecn
• 0
0
votes
1
reply
4.6k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 18 months ago by
James W. MacDonald
67k • written 18 months ago by
chiwut.wong
• 0
1
vote
1
reply
720
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 19 months ago by
ATpoint
★ 4.6k • written 19 months ago by
khaserdene99
• 0
0
votes
1
reply
1.0k
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 19 months ago by
ATpoint
★ 4.6k • written 19 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.8k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 9 months ago by
Ashley
• 0 • written 19 months ago by
zxc741xb
• 0
3
votes
6
replies
1.2k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 19 months ago by
Gordon Smyth
52k • written 20 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
752
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 19 months ago by
Michael Love
43k • written 20 months ago by
suphamon.j
▴ 20
2
votes
1
reply
846
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 20 months ago by
andres.firrincieli
▴ 50 • written 20 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
601
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
20 months ago
Levi
• 0
3
votes
7
replies
1.8k
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
20 months ago
Ortega-C
▴ 10
0
votes
1
reply
709
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 20 months ago by
ATpoint
★ 4.6k • written 20 months ago by
Adam
• 0
0
votes
0
replies
744
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
21 months ago
Ortega-C
▴ 10
0
votes
2
replies
835
views
WGCNA problem
WGCNA
updated 21 months ago by
Ortega-C
▴ 10 • written 21 months ago by
mortezaali
• 0
0
votes
0
replies
756
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
21 months ago
Levi
• 0
0
votes
0
replies
632
views
Module Trait Corelation
WGCNA
22 months ago
allanokwaro
• 0
2
votes
3
replies
1.3k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 22 months ago by
ATpoint
★ 4.6k • written 22 months ago by
suphamon.j
▴ 20
0
votes
0
replies
683
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
23 months ago
Sooni
▴ 10
0
votes
0
replies
688
views
Multiple way network preservation
wgcna
23 months ago
madzayasodara
• 0
0
votes
0
replies
762
views
WGCNA TOM file empty
WGCNA
TOM
23 months ago
gianni.drm
• 0
0
votes
0
replies
1.2k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
23 months ago
gianni.drm
• 0
0
votes
1
reply
1.3k
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 10 months ago by
boczniak767
▴ 740 • written 23 months ago by
Kim
• 0
0
votes
1
reply
683
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 24 months ago by
andres.firrincieli
▴ 50 • written 24 months ago by
S
• 0
0
votes
0
replies
824
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
24 months ago
S
• 0
0
votes
0
replies
808
views
Problems running WGCNA
WGCNA
2.1 years ago
S
• 0
0
votes
0
replies
680
views
coexpression networks
WGCNA
igraph
2.1 years ago
María José
• 0
0
votes
0
replies
743
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
2.1 years ago
Abdullah
• 0
50 results • Page
1 of 1
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Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression?
by
Peter Hickey
▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
by
QN
▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs
by
ATpoint
★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA?
by
ATpoint
★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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