Showing : Network • reset
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News: Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology Bioconductor Network
11 months ago info ▴ 10
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1
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934
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 15 months ago by ★ 4.8k • written 15 months ago by • 0
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1
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1.3k
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How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 15 months ago by ▴ 30 • written 16 months ago by ▴ 90
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2
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941
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
16 months ago Luca • 0
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2
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2.1k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 11 months ago by • 0 • written 2.4 years ago by • 0
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10
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2.7k
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Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 2.4 years ago by • 0
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1
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4.9k
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Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 21 months ago by 68k • written 21 months ago by • 0
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893
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
21 months ago info ▴ 10
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3
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1.0k
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
21 months ago Alexandros • 0
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1.3k
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WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.4 years ago • updated 6 months ago bioinformaticssrm2011 • 0
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1.1k
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Gene co-expression network analysis with small sample size
Network
2.5 years ago Senthil • 0
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779
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
2.6 years ago Julieta • 0
2
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1
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1.1k
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WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 2.6 years ago by ▴ 50 • written 2.6 years ago by ▴ 10
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1
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1.7k
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WGCNA: Obtaining a consensus network from sampledBlockwiseModules function output
Network consensus sampledBlockwiseModules resampling WGCNA
updated 3.2 years ago by ★ 3.0k • written 3.3 years ago by ▴ 30
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1.3k
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Trouble with gene dendrogram
Network RNASeq WGCNA
updated 2.3 years ago by • 0 • written 3.4 years ago by ▴ 10
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1.1k
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WGCNA error during network construction
WGCNA Network R
3.6 years ago gitanjali • 0
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1
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2.6k
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Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
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Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
4.1 years ago martin.schaefer • 0
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0
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.3 years ago jol.espinoz ▴ 40
15
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17
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28k
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WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 4.4 years ago by ▴ 760 • written 8.6 years ago by ▴ 40
4
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2
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1.4k
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iSEE - Custom Panel
Network GeneNetwork iSEE
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
3
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3
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7.3k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 10 days ago by • 0 • written 4.7 years ago by ▴ 80
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2
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2.9k
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Soft-threshold in WGCNA
wgcna network bicor threshold
updated 4.7 years ago by ★ 3.0k • written 4.7 years ago by ▴ 80
2
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0
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735
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Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
4.9 years ago hamza_karakurt ▴ 60
5
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2
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6.3k
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[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 30
2
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4
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2.5k
views
Case-control study using WGCNA
wgcna network rna-seq
5.4 years ago Arindam ▴ 80
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1
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2.2k
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WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 5.6 years ago by 52k • written 5.6 years ago by ▴ 10
2
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1
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2.0k
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Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
4
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3
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1.3k
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WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 6.0 years ago by ★ 3.0k • written 6.0 years ago by ▴ 80
7
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9
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5.5k
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WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.3 years ago by ★ 3.0k • written 6.0 years ago by ▴ 10
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1
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2.0k
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igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 3.7 years ago by 52k • written 6.1 years ago by • 0
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0
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1.1k
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Help with creating tumor cell line network
nci network
6.9 years ago torgeirous • 0
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0
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1.3k
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Help with generating network from gene expression data
gene expression network cytoscape
7.3 years ago torgeirous • 0
1
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1
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1.7k
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Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 7.5 years ago by ▴ 760 • written 7.6 years ago by ▴ 40
1
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1
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1.8k
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Custom scoring for subnetworks in BioNet
bionet network
updated 8.9 years ago by ▴ 120 • written 8.9 years ago by ▴ 680
1
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2
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1.6k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 8.9 years ago by ▴ 120 • written 8.9 years ago by ▴ 680
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2
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3.1k
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WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.3 years ago hywel.williams • 0
5
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14
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5.6k
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Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 9.4 years ago by ★ 8.2k • written 9.4 years ago by ▴ 50
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0
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1.4k
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Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
9.5 years ago kbastard • 0
2
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5
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1.7k
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runing NetBenchmark on my own datasets
software error network
updated 9.5 years ago by ▴ 20 • written 9.5 years ago by ▴ 40
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0
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1.5k
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PSICQUIC: Direction of interaction
network protein interaction analysis
9.8 years ago kmezhoud ▴ 10
1
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2
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3.5k
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cnetplot() - library(clusterProfiler)
clusterProfiler network
9.9 years ago cristina della beffa ▴ 30
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0
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1.7k
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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
10.3 years ago Thomas.F.Hahn2 • 0
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3.1k
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Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.5 years ago pshannon ▴ 100
1
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2
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4.6k
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Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 10.6 years ago by ▴ 180 • written 10.6 years ago by ▴ 260
2
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6
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5.5k
views
Error running TOMplot in WGCNA package
wgcna network
updated 10.6 years ago by ▴ 180 • written 10.6 years ago by ▴ 260
7
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1
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4.0k
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Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 10.6 years ago by ★ 13k • written 10.6 years ago by ▴ 260
8
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4
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7.8k
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WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 10.6 years ago by ★ 3.0k • written 10.6 years ago by ▴ 180
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0
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1.3k
views
回复： XVector
Network Cancer IRanges XVector
10.6 years ago Hervé Pagès 16k
1
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1
reply
1.6k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 10.8 years ago by ★ 3.0k • written 10.8 years ago by ▴ 130
50 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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Scholar to Gordon Smyth 52k
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