Showing : network • reset
1
vote
10
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836
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Interprteting the phylogenomic profiles plot
syntenet synteny Network
updated 26 days ago by • 0 • written 6 months ago by • 0
0
votes
0
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233
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
6 months ago pharamac • 0
0
votes
0
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252
views
WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
6 months ago bioinformaticssrm2011 • 0
0
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0
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291
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Gene co-expression network analysis with small sample size
Network
7 months ago Senthil • 0
0
votes
0
replies
207
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
8 months ago Julieta • 0
2
votes
1
reply
318
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 8 months ago by ▴ 50 • written 8 months ago by ▴ 10
0
votes
1
reply
590
views
WGCNA: Obtaining a consensus network from sampledBlockwiseModules function output
Network consensus sampledBlockwiseModules resampling WGCNA
updated 16 months ago by ★ 2.8k • written 17 months ago by ▴ 30
0
votes
1
reply
569
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 4 months ago by • 0 • written 18 months ago by • 0
0
votes
0
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410
views
WGCNA error during network construction
WGCNA Network R
20 months ago gitanjali • 0
0
votes
1
reply
1.0k
views
Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 24 months ago by 3.8k • written 24 months ago by • 0
0
votes
0
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543
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
2.2 years ago martin.schaefer • 0
0
votes
0
replies
735
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
2.4 years ago jol.espinoz ▴ 40
15
votes
17
replies
19k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 2.5 years ago by ▴ 710 • written 6.7 years ago by ▴ 40
4
votes
2
replies
759
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 2.6 years ago by ★ 28k • written 2.6 years ago by • 0
3
votes
2
replies
3.3k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 12 months ago by ▴ 10 • written 2.8 years ago by ▴ 80
0
votes
2
replies
1.2k
views
Soft-threshold in WGCNA
wgcna network bicor threshold
updated 2.8 years ago by ★ 2.8k • written 2.8 years ago by ▴ 80
2
votes
0
replies
292
views
Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
3.0 years ago hamza_karakurt ▴ 50
5
votes
2
replies
2.6k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 3.3 years ago by 3.8k • written 3.3 years ago by ▴ 30
2
votes
4
replies
1.1k
views
Case-control study using WGCNA
wgcna network rna-seq
3.5 years ago ag1805x ▴ 80
1
vote
1
reply
928
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 3.7 years ago by 47k • written 3.7 years ago by ▴ 10
2
votes
1
reply
994
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 4.0 years ago by 40k • written 4.0 years ago by • 0
2
votes
3
replies
600
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 4.1 years ago by ★ 2.8k • written 4.1 years ago by ▴ 80
7
votes
9
replies
2.3k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 4 months ago by ★ 2.8k • written 4.1 years ago by ▴ 10
0
votes
1
reply
1.1k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 21 months ago by 47k • written 4.2 years ago by • 0
0
votes
0
replies
572
views
Help with creating tumor cell line network
nci network
5.0 years ago torgeirous • 0
0
votes
0
replies
723
views
Help with generating network from gene expression data
gene expression network cytoscape
5.4 years ago torgeirous • 0
1
vote
1
reply
833
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 5.6 years ago by ▴ 710 • written 5.7 years ago by ▴ 40
1
vote
1
reply
1.2k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 7.0 years ago by ▴ 120 • written 7.0 years ago by ▴ 660
1
vote
2
replies
1.0k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 7.0 years ago by ▴ 120 • written 7.0 years ago by ▴ 660
0
votes
2
replies
2.3k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
7.4 years ago hywel.williams • 0
5
votes
14
replies
4.0k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 7.5 years ago by ★ 8.2k • written 7.5 years ago by ▴ 50
0
votes
0
replies
981
views
Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
7.6 years ago kbastard • 0
2
votes
5
replies
1.1k
views
runing NetBenchmark on my own datasets
software error network
updated 7.6 years ago by ▴ 20 • written 7.6 years ago by ▴ 40
0
votes
0
replies
991
views
PSICQUIC: Direction of interaction
network protein interaction analysis
7.9 years ago kmezhoud ▴ 10
1
vote
2
replies
2.3k
views
cnetplot() - library(clusterProfiler)
clusterProfiler network
8.0 years ago cristina della beffa ▴ 30
0
votes
0
replies
1.2k
views
Job: Help with finding R tutors for microarray analysis, next generation sequencing and constructing gene interaction networks needed
bioconductor microarray network tutoring differential gene expression Job
8.4 years ago Thomas.F.Hahn2 • 0
1
vote
7
replies
2.3k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
8.6 years ago pshannon ▴ 100
1
vote
2
replies
3.5k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 8.7 years ago by ▴ 180 • written 8.7 years ago by ▴ 240
2
votes
6
replies
4.0k
views
Error running TOMplot in WGCNA package
wgcna network
updated 8.7 years ago by ▴ 180 • written 8.7 years ago by ▴ 240
7
votes
1
reply
3.1k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 8.7 years ago by 13k • written 8.7 years ago by ▴ 240
8
votes
4
replies
6.0k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 8.7 years ago by ★ 2.8k • written 8.7 years ago by ▴ 180
0
votes
0
replies
927
views
回复： XVector
Network Cancer IRanges XVector
8.7 years ago Hervé Pagès 16k
1
vote
1
reply
1.2k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 8.9 years ago by ★ 2.8k • written 8.9 years ago by ▴ 130
0
votes
1
reply
1.3k
views
WGCNA_ problem in creating scale free topology plot
Network Network
updated 9.0 years ago by 63k • written 9.0 years ago by ▴ 130
0
votes
0
replies
1.1k
views
PostDoc opportunity
Pathways Network Pathways Network
9.0 years ago Guest User ★ 12k
0
votes
0
replies
1.8k
views
Pathview question
Network convert pathview Network convert pathview
9.1 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
5.1k
views
WGCNA package
Network Network
updated 9.2 years ago by ★ 2.8k • written 9.2 years ago by ▴ 130
0
votes
0
replies
1.7k
views
IdeogramTrack and bigWig file errors in Gviz
GO Network rtracklayer CAMERA Gviz GO Network rtracklayer CAMERA Gviz
9.2 years ago Robert Ivanek ▴ 730
0
votes
0
replies
744
views
tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
Network Network
9.4 years ago Paul Shannon ▴ 750
0
votes
0
replies
893
views
RCytoscape: tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
SystemsBiology Network RCytoscape SystemsBiology Network RCytoscape
9.4 years ago Paul Shannon ▴ 750
50 results • Page 1 of 1
Recent ...
Replies
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would do the job.
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0
Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.
Votes
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
Comment: Question on constructing design matrix and defining contrasts for analysis
Comment: Question on constructing design matrix and defining contrasts for analysis
Answer: Question on constructing design matrix and defining contrasts for analysis
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