Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
WGCNA
•
reset
3
votes
4
replies
92
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata
Normalization_method
WGCNA
14 hours ago • updated 9 hours ago
sukeshinik5
▴ 20
0
votes
1
reply
121
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 6 days ago by
Lluís Revilla Sancho
▴ 750 • written 6 days ago by
Nasim
• 0
0
votes
0
replies
135
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
23 days ago
Fernanda
• 0
0
votes
1
reply
212
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 4 weeks ago by
Lluís Revilla Sancho
▴ 750 • written 4 weeks ago by
emilymily77
• 0
0
votes
1
reply
211
views
Ideal approach to adjust for covariates for WGCNA
WGCNA
wgcna
updated 4 weeks ago by
James W. MacDonald
67k • written 5 weeks ago by
bioinformaticssrm2011
• 0
0
votes
6
replies
2.4k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 18 months ago by
mauricio.microbiol
• 0
1
vote
3
replies
3.3k
views
WGNCA kME vs. kIM
WGCNA
updated 4 months ago by
Vitor
• 0 • written 9.1 years ago by
akridgerunner
▴ 30
0
votes
0
replies
217
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq
WGCNA
5 months ago
k200987
• 0
0
votes
2
replies
430
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
6 months ago
Gimena
• 0
0
votes
2
replies
495
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
6 months ago
w.cookson
• 0
0
votes
1
reply
346
views
problem with ClusterRepro function
WGCNA
updated 7 months ago by
James W. MacDonald
67k • written 7 months ago by
Antonio.Aubry
• 0
0
votes
1
reply
645
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor
WGCNA
updated 8 months ago by
ATpoint
★ 4.5k • written 8 months ago by
Priya
• 0
0
votes
2
replies
911
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 10 months ago by
aehall26
• 0
4
votes
3
replies
1.7k
views
WGCNA documentation not available
WGCNA
written 10 months ago by
ramonmassoni
▴ 10
0
votes
2
replies
1.4k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 5 months ago by
mariakenneth147
• 0 • written 22 months ago by
pharamac
• 0
0
votes
1
reply
1.2k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub
correlation
eigen
WGCNA
updated 10 months ago by
Vanatta
• 0 • written 2.8 years ago by
mairah.khan
• 0
1
vote
2
replies
1.0k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData
WGCNA
consensusnetworks
10 months ago • updated 9 months ago
Levi
• 0
0
votes
2
replies
494
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
10 months ago
davca
• 0
0
votes
1
reply
691
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 11 months ago by
ATpoint
★ 4.5k • written 11 months ago by
ellen.francis
• 0
1
vote
1
reply
626
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 11 months ago by
tangming2005
▴ 200 • written 11 months ago by
meenae
▴ 10
0
votes
1
reply
547
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr
WGCNA
updated 14 months ago by
ATpoint
★ 4.5k • written 14 months ago by
jiecn
• 0
0
votes
1
reply
3.8k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 14 months ago by
James W. MacDonald
67k • written 14 months ago by
chiwut.wong
• 0
1
vote
1
reply
667
views
WGCNA Cluster batch effect
BatchEffect
TCGA
WGCNA
updated 15 months ago by
ATpoint
★ 4.5k • written 15 months ago by
khaserdene99
• 0
0
votes
1
reply
880
views
Hub genes selection in WGCNA
wgcna
WGCNA
hubgene
updated 16 months ago by
ATpoint
★ 4.5k • written 16 months ago by
suphamon.j
▴ 20
2
votes
5
replies
1.6k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 6 months ago by
Ashley
• 0 • written 16 months ago by
zxc741xb
• 0
3
votes
6
replies
1.1k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 16 months ago by
Gordon Smyth
51k • written 16 months ago by
mohammedtoufiq91
▴ 10
1
vote
0
replies
682
views
WGCNA of two different cohorts study
DifferentialExpression
WGCNA
updated 16 months ago by
Michael Love
42k • written 16 months ago by
suphamon.j
▴ 20
2
votes
1
reply
738
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
wgcna_package
updated 16 months ago by
andres.firrincieli
▴ 50 • written 16 months ago by
hesse.sebastian
▴ 10
0
votes
0
replies
542
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules
WGCNA
consensus
16 months ago
Levi
• 0
3
votes
7
replies
1.6k
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
17 months ago
Ortega-C
▴ 10
0
votes
1
reply
644
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 17 months ago by
ATpoint
★ 4.5k • written 17 months ago by
Adam
• 0
0
votes
0
replies
685
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana
removeisoforms
WGCNA
18 months ago • updated 17 months ago
Ortega-C
▴ 10
0
votes
2
replies
769
views
WGCNA problem
WGCNA
updated 17 months ago by
Ortega-C
▴ 10 • written 18 months ago by
mortezaali
• 0
0
votes
0
replies
692
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome
RNAseq
WGCNA
18 months ago
Levi
• 0
0
votes
0
replies
561
views
Module Trait Corelation
WGCNA
19 months ago
allanokwaro
• 0
2
votes
3
replies
1.2k
views
Batch correction and Deseq2
DESeq2
WGCNA
Normalization
NormalyzerDE
BatchEffect
updated 19 months ago by
ATpoint
★ 4.5k • written 19 months ago by
suphamon.j
▴ 20
0
votes
0
replies
605
views
How to draw module significance barplot?
module_significance
barplot
WGCNA
20 months ago
Sooni
▴ 10
0
votes
0
replies
621
views
Multiple way network preservation
wgcna
20 months ago
madzayasodara
• 0
0
votes
0
replies
705
views
WGCNA TOM file empty
WGCNA
TOM
20 months ago
gianni.drm
• 0
0
votes
0
replies
1.1k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape
Heatmap
heatmaps
WGCNA
20 months ago
gianni.drm
• 0
0
votes
1
reply
1.2k
views
WGCNA soft thresholding suggesting a power of 1
independence
thresholding
WGCNA
connectivity
scale
updated 7 months ago by
boczniak767
▴ 740 • written 20 months ago by
Kim
• 0
0
votes
1
reply
640
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 20 months ago by
andres.firrincieli
▴ 50 • written 20 months ago by
S
• 0
0
votes
0
replies
751
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
21 months ago
S
• 0
0
votes
0
replies
743
views
Problems running WGCNA
WGCNA
22 months ago
S
• 0
0
votes
0
replies
637
views
coexpression networks
WGCNA
igraph
22 months ago
María José
• 0
0
votes
0
replies
692
views
A question about GWENA R/Bioconductor package
proteomics
GWENA
Proteomics
WGCNA
22 months ago
Abdullah
• 0
0
votes
0
replies
1.0k
views
WGCNA: minModuleSize is not responding correctly
Network
minModuleSize
WGCNA
wgcna
23 months ago • updated 17 days ago
bioinformaticssrm2011
• 0
2
votes
1
reply
974
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 2.1 years ago by
andres.firrincieli
▴ 50 • written 2.1 years ago by
ikumar2000
▴ 10
0
votes
1
reply
1.0k
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 2.1 years ago by
andres.firrincieli
▴ 50 • written 2.1 years ago by
Recep
▴ 20
0
votes
0
replies
677
views
MM-GS plot doesn't show any negative correlation
wgcna
2.2 years ago
shubhankar.pawar
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to reverse complement some elements of a DNAStringSet
by
Christine Jones
• 0
Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts?
by
Katherine
• 0
Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect. the ```normalized_counts``` variable …
Answer: How to reverse complement some elements of a DNAStringSet
by
James W. MacDonald
67k
You should always try the vectorized method first, rather than looping. ``` > myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…
Answer: When running contrasts, does it use normalized read counts?
by
James W. MacDonald
67k
A contrast is a comparison of two or more coefficients. When you run `nbiomWaldTest` you are fitting the GLM and estimating coefficients. T…
Comment: Too much data for Diffbind
by
Ou, Jianhong
★ 1.3k
Just in case if somebody still want to apply summits greater than 0 and got the same error, you can filter out the peaks with start positio…
Votes
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
What should be the normalization protocol for RNA seq data for WGCNA?
Awards
• All
Scholar
to
James W. MacDonald
67k
Popular Question
to
shepherl
4.0k
Scholar
to
Gordon Smyth
51k
Popular Question
to
bioinformaticssrm2011
• 0
Popular Question
to
sukeshinik5
▴ 20
Locations
• All
France,
14 minutes ago
United States,
1 hour ago
France,
2 hours ago
United States,
2 hours ago
Iran,
2 hours ago
Traffic: 578 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6