Showing : network • reset
3
votes
4
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7.8k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.1 years ago by ▴ 80
0
votes
0
replies
585
views
News: Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology Bioconductor Network
15 months ago info ▴ 10
0
votes
1
reply
1.1k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 19 months ago by ★ 4.9k • written 19 months ago by • 0
1
vote
1
reply
1.4k
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 20 months ago by ▴ 30 • written 20 months ago by ▴ 90
0
votes
2
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1.1k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
21 months ago • updated 20 months ago Luca • 0
0
votes
2
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2.4k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 15 months ago by • 0 • written 2.8 years ago by • 0
1
vote
10
replies
2.9k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 2.8 years ago by • 0
0
votes
1
reply
5.0k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
0
replies
990
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
2.1 years ago info ▴ 10
0
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3
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1.2k
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
2.2 years ago Alexandros • 0
0
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0
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1.4k
views
WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.8 years ago • updated 11 months ago bioinformaticssrm2011 • 0
0
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0
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1.2k
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Gene co-expression network analysis with small sample size
Network
2.9 years ago Senthil • 0
0
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0
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1.0k
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
3.0 years ago Julieta • 0
2
votes
1
reply
1.2k
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 3.0 years ago by ▴ 50 • written 3.0 years ago by ▴ 10
0
votes
1
reply
1.8k
views
WGCNA: Obtaining a consensus network from sampledBlockwiseModules function output
Network consensus sampledBlockwiseModules resampling WGCNA
updated 3.6 years ago by ★ 3.0k • written 3.7 years ago by ▴ 30
0
votes
1
reply
1.4k
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 2.6 years ago by • 0 • written 3.8 years ago by ▴ 10
0
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0
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1.2k
views
WGCNA error during network construction
WGCNA Network R
3.9 years ago gitanjali • 0
0
votes
1
reply
3.0k
views
Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
0
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0
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1.2k
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
4.4 years ago martin.schaefer • 0
0
votes
0
replies
1.6k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.6 years ago jol.espinoz ▴ 40
15
votes
17
replies
30k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 4.8 years ago by ▴ 760 • written 9.0 years ago by ▴ 40
4
votes
2
replies
1.5k
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 4.8 years ago by ★ 29k • written 4.8 years ago by • 0
0
votes
2
replies
3.1k
views
Soft-threshold in WGCNA
wgcna network bicor threshold
updated 5.1 years ago by ★ 3.0k • written 5.1 years ago by ▴ 80
2
votes
0
replies
785
views
Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
5.2 years ago hamza_karakurt ▴ 60
5
votes
2
replies
6.7k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 5.6 years ago by ★ 4.0k • written 5.6 years ago by ▴ 30
2
votes
4
replies
2.7k
views
Case-control study using WGCNA
wgcna network rna-seq
5.7 years ago Arindam ▴ 80
1
vote
1
reply
2.3k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 6.0 years ago by 52k • written 6.0 years ago by ▴ 10
2
votes
1
reply
2.0k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
4
votes
3
replies
1.3k
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 6.3 years ago by ★ 3.0k • written 6.3 years ago by ▴ 80
7
votes
9
replies
5.9k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.6 years ago by ★ 3.0k • written 6.3 years ago by ▴ 10
0
votes
1
reply
2.1k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 4.1 years ago by 52k • written 6.4 years ago by • 0
0
votes
0
replies
1.1k
views
Help with creating tumor cell line network
nci network
7.2 years ago torgeirous • 0
0
votes
0
replies
1.4k
views
Help with generating network from gene expression data
gene expression network cytoscape
7.6 years ago torgeirous • 0
1
vote
1
reply
1.8k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 7.9 years ago by ▴ 760 • written 7.9 years ago by ▴ 40
1
vote
1
reply
1.9k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 9.2 years ago by ▴ 120 • written 9.2 years ago by ▴ 680
1
vote
2
replies
1.7k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 9.2 years ago by ▴ 120 • written 9.2 years ago by ▴ 680
0
votes
2
replies
3.2k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.6 years ago hywel.williams • 0
5
votes
14
replies
5.9k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by ▴ 50
0
votes
0
replies
1.5k
views
Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
9.8 years ago kbastard • 0
2
votes
5
replies
1.8k
views
runing NetBenchmark on my own datasets
software error network
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by ▴ 40
0
votes
0
replies
1.5k
views
PSICQUIC: Direction of interaction
network protein interaction analysis
10.2 years ago kmezhoud ▴ 10
1
vote
2
replies
3.6k
views
cnetplot() - library(clusterProfiler)
clusterProfiler network
10.2 years ago cristina della beffa ▴ 30
0
votes
0
replies
1.8k
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
10.7 years ago Thomas.F.Hahn2 • 0
1
vote
7
replies
3.3k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.8 years ago pshannon ▴ 100
1
vote
2
replies
4.7k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 10.9 years ago by ▴ 180 • written 10.9 years ago by ▴ 270
2
votes
6
replies
5.6k
views
Error running TOMplot in WGCNA package
wgcna network
updated 10.9 years ago by ▴ 180 • written 10.9 years ago by ▴ 270
7
votes
1
reply
4.1k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 11.0 years ago by ★ 13k • written 11.0 years ago by ▴ 270
8
votes
4
replies
8.0k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 11.0 years ago by ★ 3.0k • written 11.0 years ago by ▴ 180
0
votes
0
replies
1.3k
views
回复： XVector
Network Cancer IRanges XVector
11.0 years ago Hervé Pagès 16k
1
vote
1
reply
1.7k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 11.2 years ago by ★ 3.0k • written 11.2 years ago by ▴ 130
180 results • Page 1 of 4
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Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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