Showing : network • reset
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News: Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology Bioconductor Network
8 months ago info ▴ 10
0
votes
1
reply
787
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
1
vote
1
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1.2k
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 12 months ago by ▴ 30 • written 13 months ago by ▴ 90
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2
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788
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
13 months ago Luca • 0
0
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2
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1.7k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 8 months ago by • 0 • written 2.2 years ago by • 0
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10
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2.6k
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Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 2.2 years ago by • 0
0
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1
reply
4.6k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 18 months ago by 67k • written 18 months ago by • 0
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0
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798
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
18 months ago info ▴ 10
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3
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874
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
18 months ago Alexandros • 0
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0
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1.1k
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WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.2 years ago • updated 3 months ago bioinformaticssrm2011 • 0
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0
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991
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Gene co-expression network analysis with small sample size
Network
2.3 years ago Senthil • 0
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713
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
2.3 years ago Julieta • 0
2
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1
reply
1.0k
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WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 2.3 years ago by ▴ 50 • written 2.3 years ago by ▴ 10
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1
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1.6k
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WGCNA: Obtaining a consensus network from sampledBlockwiseModules function output
Network consensus sampledBlockwiseModules resampling WGCNA
updated 3.0 years ago by ★ 3.0k • written 3.0 years ago by ▴ 30
0
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1
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1.2k
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Trouble with gene dendrogram
Network RNASeq WGCNA
updated 2.0 years ago by • 0 • written 3.1 years ago by ▴ 10
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0
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1.0k
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WGCNA error during network construction
WGCNA Network R
3.3 years ago gitanjali • 0
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1
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2.2k
views
Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
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0
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1.0k
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Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.8 years ago martin.schaefer • 0
0
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0
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1.5k
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.0 years ago jol.espinoz ▴ 40
15
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17
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27k
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WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 4.1 years ago by ▴ 760 • written 8.4 years ago by ▴ 40
4
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2
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1.3k
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 4.2 years ago by ★ 28k • written 4.2 years ago by • 0
3
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2
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6.6k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 2.7 years ago by ▴ 10 • written 4.4 years ago by ▴ 80
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2
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2.7k
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Soft-threshold in WGCNA
wgcna network bicor threshold
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 80
2
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0
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673
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Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
4.6 years ago hamza_karakurt ▴ 60
5
votes
2
replies
5.5k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 30
2
votes
4
replies
2.3k
views
Case-control study using WGCNA
wgcna network rna-seq
5.1 years ago Arindam ▴ 80
1
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1
reply
2.0k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 5.4 years ago by 52k • written 5.4 years ago by ▴ 10
2
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1
reply
1.8k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
4
votes
3
replies
1.2k
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 80
7
votes
9
replies
4.9k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.0 years ago by ★ 3.0k • written 5.7 years ago by ▴ 10
0
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1
reply
1.9k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 3.4 years ago by 52k • written 5.8 years ago by • 0
0
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0
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1.0k
views
Help with creating tumor cell line network
nci network
6.6 years ago torgeirous • 0
0
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0
replies
1.3k
views
Help with generating network from gene expression data
gene expression network cytoscape
7.0 years ago torgeirous • 0
1
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1
reply
1.6k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 7.2 years ago by ▴ 760 • written 7.3 years ago by ▴ 40
1
vote
1
reply
1.7k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 8.6 years ago by ▴ 120 • written 8.6 years ago by ▴ 660
1
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2
replies
1.5k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 8.6 years ago by ▴ 120 • written 8.6 years ago by ▴ 660
0
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2
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3.0k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.0 years ago hywel.williams • 0
5
votes
14
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5.4k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 9.1 years ago by ★ 8.2k • written 9.1 years ago by ▴ 50
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0
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1.3k
views
Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
9.2 years ago kbastard • 0
2
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5
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1.6k
views
runing NetBenchmark on my own datasets
software error network
updated 9.3 years ago by ▴ 20 • written 9.3 years ago by ▴ 40
0
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0
replies
1.4k
views
PSICQUIC: Direction of interaction
network protein interaction analysis
9.5 years ago kmezhoud ▴ 10
1
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2
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3.3k
views
cnetplot() - library(clusterProfiler)
clusterProfiler network
9.6 years ago cristina della beffa ▴ 30
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0
replies
1.7k
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
10.1 years ago Thomas.F.Hahn2 • 0
1
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7
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3.0k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.2 years ago pshannon ▴ 100
1
vote
2
replies
4.4k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 10.3 years ago by ▴ 180 • written 10.3 years ago by ▴ 260
2
votes
6
replies
5.2k
views
Error running TOMplot in WGCNA package
wgcna network
updated 10.3 years ago by ▴ 180 • written 10.3 years ago by ▴ 260
7
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1
reply
3.8k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 10.3 years ago by ★ 13k • written 10.3 years ago by ▴ 260
8
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4
replies
7.5k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 10.4 years ago by ★ 3.0k • written 10.4 years ago by ▴ 180
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0
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1.3k
views
回复： XVector
Network Cancer IRanges XVector
10.4 years ago Hervé Pagès 16k
1
vote
1
reply
1.6k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 10.6 years ago by ★ 3.0k • written 10.6 years ago by ▴ 130
50 results • Page 1 of 1
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Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Comment: EdgeR Biological CVs by Joseph ▴ 10
I believe the published study provides answers to your questions. Yunshun Chen and Pedro Baldoni's recent papers on edgeR may also be of in…
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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Comment: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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