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wgcna
•
reset
0
votes
5
replies
1.6k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by
mauricio.microbiol
• 0
0
votes
2
replies
162
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
16 days ago • updated 15 days ago
Gimena
• 0
0
votes
2
replies
204
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
21 days ago • updated 16 days ago
w.cookson
• 0
0
votes
1
reply
155
views
problem with ClusterRepro function
WGCNA
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Antonio.Aubry
• 0
0
votes
1
reply
233
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 10 weeks ago by
ATpoint
★ 4.0k • written 10 weeks ago by
Priya
• 0
0
votes
2
replies
471
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 4 months ago by
aehall26
• 0
4
votes
3
replies
825
views
WGCNA documentation not available
WGCNA
written 4 months ago by
ramonmassoni
▴ 10
0
votes
1
reply
855
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
979
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
1
vote
2
replies
638
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
4 months ago • updated 3 months ago
Levi
• 0
0
votes
2
replies
296
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
4 months ago
davca
• 0
0
votes
1
reply
470
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
ellen.francis
• 0
1
vote
1
reply
379
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 5 months ago by
tangming2005
▴ 190 • written 5 months ago by
meenae
▴ 10
0
votes
1
reply
372
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
jiecn
• 0
0
votes
1
reply
1.8k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
chiwut.wong
• 0
1
vote
1
reply
476
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 9 months ago by
ATpoint
★ 4.0k • written 9 months ago by
khaserdene99
• 0
0
votes
1
reply
579
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 1 day ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
3
votes
6
replies
814
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
452
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 10 months ago by
Michael Love
41k • written 10 months ago by
suphamon.j
▴ 20
2
votes
1
reply
487
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 10 months ago by
andres.firrincieli
▴ 50 • written 10 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
407
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
11 months ago
Levi
• 0
1
vote
2
replies
2.6k
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
1.1k
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
513
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 11 months ago by
ATpoint
★ 4.0k • written 11 months ago by
Adam
• 0
0
votes
0
replies
529
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
12 months ago • updated 11 months ago
Ortega-C
▴ 10
0
votes
2
replies
587
views
WGCNA problem
WGCNA
updated 11 months ago by
Ortega-C
▴ 10 • written 12 months ago by
mortezaali
• 0
0
votes
0
replies
550
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
12 months ago
Levi
• 0
0
votes
0
replies
396
views
Module Trait Corelation
WGCNA
13 months ago
allanokwaro
• 0
2
votes
3
replies
856
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
suphamon.j
▴ 20
0
votes
0
replies
423
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
14 months ago
Sooni
▴ 10
0
votes
0
replies
462
views
Multiple way network preservation
wgcna
14 months ago
madzayasodara
• 0
0
votes
0
replies
512
views
WGCNA TOM file empty
WGCNA
TOM
14 months ago
gianni.drm
• 0
0
votes
0
replies
794
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
14 months ago
gianni.drm
• 0
0
votes
1
reply
857
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 7 weeks ago by
boczniak767
▴ 720 • written 14 months ago by
Kim
• 0
0
votes
1
reply
506
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 14 months ago by
andres.firrincieli
▴ 50 • written 14 months ago by
S
• 0
0
votes
0
replies
607
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
15 months ago
S
• 0
0
votes
0
replies
578
views
Problems running WGCNA
WGCNA
16 months ago
S
• 0
0
votes
0
replies
514
views
coexpression networks
WGCNA
igraph
16 months ago
María José
• 0
0
votes
0
replies
488
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
16 months ago
Abdullah
• 0
0
votes
0
replies
723
views
WGCNA: minModuleSize is not responding correctly
wgcna
Network
WGCNA
minModuleSize
17 months ago
bioinformaticssrm2011
• 0
2
votes
1
reply
774
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 19 months ago by
andres.firrincieli
▴ 50 • written 19 months ago by
ikumar2000
▴ 10
0
votes
1
reply
798
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 19 months ago by
andres.firrincieli
▴ 50 • written 20 months ago by
Recep
▴ 20
0
votes
0
replies
547
views
MM-GS plot doesn't show any negative correlation
wgcna
21 months ago
shubhankar.pawar
• 0
0
votes
1
reply
926
views
WGCNA Export Eigengene Adjacency/Correlation values export
WGCNA
updated 21 months ago by
Cannabis Equipment Financing
• 0 • written 21 months ago by
803ebee7
• 0
0
votes
0
replies
620
views
ARACNe Sample Size
grndata
GRN
ARACNE
WGCNA
21 months ago
Harrsha
• 0
0
votes
0
replies
508
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
21 months ago
María José
• 0
0
votes
0
replies
598
views
How to create consensus network from SampledBlockwiseModules in WGCNA?
NetworkInference
SampledBlockWiseModules
WGCNA
21 months ago
as8020
• 0
0
votes
0
replies
412
views
WGCNA consensusMEDdissimilrity
WGCNA
23 months ago
María José
• 0
1
vote
3
replies
1.7k
views
WGCNA error
WGCNA
23 months ago
ayabalbaa1990
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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