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wgcna
•
reset
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 13 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 14 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
2
replies
182
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago • updated 28 days ago
Gimena
• 0
0
votes
2
replies
226
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
4 weeks ago • updated 29 days ago
w.cookson
• 0
0
votes
1
reply
168
views
problem with ClusterRepro function
WGCNA
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Antonio.Aubry
• 0
0
votes
1
reply
875
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 8 weeks ago by
boczniak767
▴ 720 • written 15 months ago by
Kim
• 0
0
votes
1
reply
262
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
Priya
• 0
0
votes
1
reply
1.0k
views
WGCNA Preservation error
preservation
WGCNA
updated 3 months ago by
Gail
• 0 • written 2.3 years ago by
Sara
• 0
0
votes
2
replies
806
views
Finding Modules with WGCNA - Collapsing Biological Replicates in Expression Data - Then Finding Eigengenes on Previously Found Modules
WGCNA
Module Detection
updated 3 months ago by
dima11i
• 0 • written 4.5 years ago by
vsa1111
• 0
1
vote
2
replies
662
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
5 months ago • updated 4 months ago
Levi
• 0
0
votes
2
replies
512
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by
aehall26
• 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.2 years ago by
panagiotis.mokos
▴ 40
0
votes
2
replies
1.3k
views
WGCNA: Picking soft threshold before and after batch effect correction for Microbial data
wgcna
WGCNA
written 2.1 years ago by
bioinformaticssrm2011
• 0
4
votes
3
replies
914
views
WGCNA documentation not available
WGCNA
written 4 months ago by
ramonmassoni
▴ 10
0
votes
1
reply
889
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 4 months ago by
janetdelvalle056
• 0 • written 17 months ago by
pharamac
• 0
0
votes
1
reply
993
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 4 months ago by
Vanatta
• 0 • written 2.4 years ago by
mairah.khan
• 0
0
votes
2
replies
309
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
5 months ago
davca
• 0
0
votes
1
reply
491
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
ellen.francis
• 0
1
vote
1
reply
402
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 6 months ago by
tangming2005
▴ 190 • written 6 months ago by
meenae
▴ 10
0
votes
1
reply
386
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
jiecn
• 0
0
votes
1
reply
2.0k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
chiwut.wong
• 0
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 4.0 years ago by
Colari19
▴ 60
1
vote
1
reply
494
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
khaserdene99
• 0
0
votes
1
reply
602
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 10 months ago by
ATpoint
★ 4.1k • written 10 months ago by
suphamon.j
▴ 20
1
vote
0
replies
469
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 11 months ago by
Michael Love
41k • written 11 months ago by
suphamon.j
▴ 20
3
votes
6
replies
837
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
2
votes
1
reply
505
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 11 months ago by
andres.firrincieli
▴ 50 • written 11 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
426
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
11 months ago
Levi
• 0
1
vote
2
replies
2.7k
views
WGNCA kME vs. kIM
WGCNA
updated 11 months ago by
brukti
• 0 • written 8.6 years ago by
akridgerunner
▴ 30
3
votes
7
replies
1.2k
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
11 months ago
Ortega-C
▴ 10
0
votes
1
reply
521
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 12 months ago by
ATpoint
★ 4.1k • written 12 months ago by
Adam
• 0
0
votes
0
replies
547
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
12 months ago
Ortega-C
▴ 10
0
votes
2
replies
606
views
WGCNA problem
WGCNA
updated 12 months ago by
Ortega-C
▴ 10 • written 12 months ago by
mortezaali
• 0
0
votes
0
replies
565
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
13 months ago
Levi
• 0
0
votes
4
replies
3.9k
views
WGCNA grey module
WGCNA
updated 13 months ago by
Abir.khazaal
▴ 10 • written 6.0 years ago by
amnahsiddiqa
▴ 10
2
votes
3
replies
889
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.1k • written 13 months ago by
suphamon.j
▴ 20
0
votes
0
replies
419
views
Module Trait Corelation
WGCNA
13 months ago
allanokwaro
• 0
0
votes
2
replies
1.9k
views
WGCNA adjust p value
WGCNA
written 2.8 years ago by
jason.taotaotan
▴ 40
0
votes
0
replies
437
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
14 months ago
Sooni
▴ 10
0
votes
0
replies
484
views
Multiple way network preservation
wgcna
14 months ago
madzayasodara
• 0
0
votes
0
replies
528
views
WGCNA TOM file empty
WGCNA
TOM
14 months ago
gianni.drm
• 0
0
votes
0
replies
815
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
14 months ago
gianni.drm
• 0
0
votes
1
reply
527
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 15 months ago by
andres.firrincieli
▴ 50 • written 15 months ago by
S
• 0
0
votes
0
replies
618
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago
S
• 0
7
votes
9
replies
3.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA
R
network
co-expression
updated 15 months ago by
Peter Langfelder
★ 3.0k • written 5.0 years ago by
avelarbio46
▴ 10
0
votes
4
replies
1.6k
views
WGCNA soft threshold with methylation data but no scale-free topology
methylation
EPIC
scale-free topology
WGCNA
updated 15 months ago by
shuo
• 0 • written 4.7 years ago by
enora.fremy
• 0
0
votes
1
reply
971
views
Trouble with gene dendrogram
Network
RNASeq
WGCNA
updated 15 months ago by
shuo
• 0 • written 2.4 years ago by
jms2520
▴ 10
0
votes
0
replies
598
views
Problems running WGCNA
WGCNA
16 months ago
S
• 0
0
votes
0
replies
526
views
coexpression networks
WGCNA
igraph
17 months ago
María José
• 0
50 results • Page
1 of 1
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Comment: limma-voom: Calculate the log-fold change in gene expression within a sample
by
xofer16091
• 0
A few more names for [dino game][1] are Dino Dun, Chrome Dino, T-Rex, Google, and No Internet games. You can play the online game on a tabl…
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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