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wgcna
•
reset
1
vote
0
replies
1.4k
views
Evaluating Hub genes in WGCNA and role of using Signed network
rnaseq
WGCNA
7.2 years ago
dorothy.jrobbert
▴ 30
0
votes
0
replies
3.1k
views
Use of bicor in WGCNA
WGCNA
wgcna package
wgcna
bicor
7.2 years ago
bekah
▴ 40
0
votes
0
replies
1.3k
views
problem for constructing Topological Overlap Matrix (TOM) in WGCNA Algorithm
wgcna
RNA-seq
Topological Overlap Matrix
7.3 years ago
modarzi
▴ 10
5
votes
7
replies
3.4k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA
RNA-seq
updated 7.3 years ago by
Peter Langfelder
★ 3.0k • written 7.3 years ago by
modarzi
▴ 10
0
votes
4
replies
5.9k
views
WGCNA grey module
WGCNA
updated 2.6 years ago by
Abir.khazaal
▴ 10 • written 7.4 years ago by
amnahsiddiqa
▴ 10
0
votes
0
replies
832
views
WGCNA , value of nPermutations, module preservation
wgcna
7.4 years ago
amnahsiddiqa
▴ 10
0
votes
0
replies
933
views
WGCNA module trait relationship
WGCNA
wgcna
7.4 years ago
amnahsiddiqa
▴ 10
1
vote
1
reply
1.6k
views
Controlling for batch after Salmon-Tximport
deseq2
wgcna
salmon
rna-seq
DESeq2
updated 7.5 years ago by
James W. MacDonald
68k • written 7.5 years ago by
mad6kj
• 0
0
votes
1
reply
830
views
WGCNA Analysis and Hub gene analysis
wgcna
7.5 years ago
nazia
• 0
2
votes
3
replies
5.7k
views
WGCNA TOMType specification
WGCNA
network analysis
Sign
8.1 years ago • updated 7.5 years ago
aurora.savino
▴ 10
0
votes
0
replies
917
views
Comparable network visualisation of consensus modules between two species
WGCNA
VisANT
network visualization
7.5 years ago
Ira
▴ 10
2
votes
4
replies
6.0k
views
WGCNA: intrepreting grey unassigned "module"?
WGCNA
rnaseq
gene expression
co-expression network
updated 7.5 years ago by
Peter Langfelder
★ 3.0k • written 7.5 years ago by
davidjameswheatcroft
▴ 10
3
votes
7
replies
3.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 7.5 years ago by
Peter Langfelder
★ 3.0k • written 7.5 years ago by
7kemZmani
▴ 10
0
votes
0
replies
1.2k
views
Drop of soft-threshold curve with high power values
wgcna
picksoftthreshold
scale-free topology
co-expression network
7.5 years ago
marcantoine.guery
• 0
1
vote
1
reply
1.3k
views
Error with the tutorial for the WGCNA package
wgcna
updated 7.5 years ago by
Peter Langfelder
★ 3.0k • written 7.5 years ago by
yepingsun80
▴ 10
0
votes
0
replies
1.2k
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
7.6 years ago
tarun2
• 0
2
votes
0
replies
2.4k
views
'Error in summary(lm1)$coefficients[2, 1] : subscript out of bounds' while running pickSoftThreshold in WGCNA
wgcna
picksoftthreshold
7.6 years ago
aditi
▴ 20
3
votes
6
replies
1.9k
views
Questions on Pigengene
Pigengene
WGCNA
updated 7.6 years ago by
Habil Zare
▴ 200 • written 7.7 years ago by
boting.m.ning
• 0
0
votes
0
replies
2.3k
views
How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna
modules
coexpression
networks
7.6 years ago
jol.espinoz
▴ 40
0
votes
0
replies
1.2k
views
How to define the top 100 hub genes in each module and find out the genes having direct connections with hub genes
WGCNA
co-expression network
RNA-Seq
7.7 years ago
wangdp123
• 0
0
votes
2
replies
2.0k
views
GOenrichmentAnalysis of WGCNA mocules in Zea mays
annotation
wgcna
package
7.7 years ago
j.baldauf
• 0
2
votes
1
reply
2.0k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 7.7 years ago by
Peter Langfelder
★ 3.0k • written 7.7 years ago by
jol.espinoz
▴ 40
0
votes
0
replies
1.7k
views
What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna
transcriptome
big data
metagenomics
gene expression
7.7 years ago
jol.espinoz
▴ 40
1
vote
1
reply
2.6k
views
WGCNA - Choosing the best threshold
wgcna
sft
picksoftthreshold
threshold
rnaseq
updated 7.8 years ago by
Peter Langfelder
★ 3.0k • written 7.8 years ago by
Fabricio Almeida-Silva
▴ 40
2
votes
0
replies
2.9k
views
WGCNA package : identification of hub genes
wgcna
7.8 years ago
bharata1803
▴ 60
2
votes
2
replies
6.1k
views
How to select mergeCutHeight in WGCNA?
WGCNA
mergeCutHeight
updated 7.8 years ago by
Peter Langfelder
★ 3.0k • written 7.8 years ago by
harelarik
▴ 60
6
votes
8
replies
11k
views
WGCNA export to cytoscape
wgcna
cytoscape
updated 7.8 years ago by
harelarik
▴ 60 • written 8.5 years ago by
2323982403
▴ 60
0
votes
0
replies
2.1k
views
How to keep track of gene names during WGCNA analysis for cutTreedynamic() and moduleEigengene()?
WGCNA
cbind
merge
match gene names and Eigengene/module/colorlabels
7.9 years ago
yifangt
▴ 20
0
votes
3
replies
3.5k
views
WGCNA error on block number related.
WGCNA
block size
subscript out of bounds
7.9 years ago
yifangt
▴ 20
1
vote
6
replies
3.1k
views
WGCNA with distance matrix only from newick data.
WGCNA
eigengene
hub genes
8.0 years ago
yifangt
▴ 20
5
votes
6
replies
8.4k
views
WGCNA - module membership via max kME?
wgcna
modules
updated 8.0 years ago by
Peter Langfelder
★ 3.0k • written 8.0 years ago by
ly.leifels
▴ 10
1
vote
1
reply
1.8k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 8.0 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.1 years ago by
jol.espinoz
▴ 40
2
votes
4
replies
2.7k
views
How to get an output from DESeq2 to be used in WGCNA package
deseq2
wgcna
updated 8.1 years ago by
Peter Langfelder
★ 3.0k • written 8.1 years ago by
prab4th
• 0
0
votes
1
reply
1.7k
views
WGNA export to external software
WGCNA
network visualization
external software
cytoscape
updated 8.1 years ago by
Peter Langfelder
★ 3.0k • written 8.1 years ago by
je.maxfield
• 0
0
votes
6
replies
1.8k
views
RNseq data for WGCNA
WGCNA
updated 8.1 years ago by
Peter Langfelder
★ 3.0k • written 8.1 years ago by
joseph
▴ 50
2
votes
2
replies
2.6k
views
WGCNA connecting trait data
WGCNA
wgcna
rownames
updated 8.1 years ago by
Peter Langfelder
★ 3.0k • written 8.1 years ago by
je.maxfield
• 0
0
votes
1
reply
1.6k
views
Meta-analysis with WGCNA
WGCNA
updated 8.1 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.1 years ago by
joseph
▴ 50
0
votes
4
replies
2.6k
views
Problem with WGCNA - Module-trait relationship
wgcna
updated 8.2 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.2 years ago by
amoltej
▴ 10
0
votes
1
reply
2.1k
views
WGCNA works on time course data
WGCNA
updated 8.2 years ago by
Peter Langfelder
★ 3.0k • written 8.2 years ago by
joseph
▴ 50
2
votes
2
replies
2.2k
views
WGCNA - module membership preservation for low count genes
wgcna
8.3 years ago
ly.leifels
▴ 10
0
votes
2
replies
1.8k
views
WGCNA: Exporting MEs with Subject/Sample Identification
WGCNA
8.3 years ago
Tox_scientist20
• 0
0
votes
0
replies
1.5k
views
Problem about functional annotation network of WGCNA modules (modified)
wgcna
network analysis
pathway analysis
8.3 years ago
panagiotis.mokos
▴ 40
0
votes
3
replies
2.8k
views
failed to use multiple threads in R via openblas
wgcna
R
openblas
blas
threads
updated 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
RC
• 0
0
votes
1
reply
2.3k
views
signed kME(MM) for finding hub genes in modules of interest
wgcna
8.4 years ago
chiayi
• 0
0
votes
2
replies
1.7k
views
WGCNA: error message in blockwiseModule(): address 0x0, cause 'memory not mapped'
wgcna
updated 8.4 years ago by
Peter Langfelder
★ 3.0k • written 8.4 years ago by
Razumall
• 0
0
votes
2
replies
1.8k
views
Normalization for comparative transcriptomics between species
deseq2
wgcna
updated 8.4 years ago by
Michael Love
43k • written 8.4 years ago by
jcfnielsen
• 0
4
votes
1
reply
2.4k
views
WGCNA always requires trait data?
wgcna
rnaseq
updated 8.4 years ago by
Steve Lianoglou
★ 13k • written 8.4 years ago by
adriana.gallego.02
▴ 20
0
votes
2
replies
2.0k
views
Intramodular connectivity RNA-seq WGCNA
wgcna
updated 8.4 years ago by
Peter Langfelder
★ 3.0k • written 8.4 years ago by
adriana.gallego.02
▴ 20
0
votes
1
reply
1.4k
views
The cor and corp values in verboseScatterplot don't match with cor, corPvalueStudent results
WGCNA
wgcna
updated 8.4 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.4 years ago by
joseph
▴ 50
1
vote
1
reply
1.3k
views
Can I apply WGCNA on unmatched time point microarray data and clinical data?
WGCNA
8.4 years ago
joseph
▴ 50
335 results • Page
5 of 7
Recent ...
Replies
Comment: bake() and cool() resulting in an empty table
by
Francesc
• 0
Hi Catherine, thanks so much for using dar and for reporting this bug! We have identified the issue and pushed a fix to the dar repo (PR #…
Comment: Using DESeq2 for age prediction
by
ATpoint
★ 5.0k
You sure will find online tutorials on regression models / machine learning classifiers. The support site is for help with Bioconductor. Ch…
Comment: Using DESeq2 for age prediction
by
picasa1983
• 0
Thanks ! Do you have any idea how to do that ?
Answer: Using DESeq2 for age prediction
by
ATpoint
★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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