Showing : Network • reset
0
votes
1
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292
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
vote
1
reply
844
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 4 months ago by ▴ 20 • written 4 months ago by ▴ 90
0
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2
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343
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
0
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1
reply
898
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 4 months ago by • 0 • written 17 months ago by • 0
1
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10
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2.0k
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Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 17 months ago by • 0
0
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1
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2.0k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 9 months ago by 65k • written 9 months ago by • 0
0
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0
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532
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
9 months ago info ▴ 10
0
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3
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574
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
10 months ago • updated 9 months ago Alexandros • 0
7
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9
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3.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 15 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
0
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1
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973
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 15 months ago by • 0 • written 2.4 years ago by ▴ 10
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0
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757
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WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
17 months ago bioinformaticssrm2011 • 0
0
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0
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738
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Gene co-expression network analysis with small sample size
Network
19 months ago Senthil • 0
0
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0
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522
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
19 months ago Julieta • 0
2
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1
reply
793
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WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 19 months ago by ▴ 50 • written 19 months ago by ▴ 10
3
votes
2
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5.1k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 23 months ago by ▴ 10 • written 3.7 years ago by ▴ 80
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1
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1.2k
views
WGCNA: Obtaining a consensus network from sampledBlockwiseModules function output
Network consensus sampledBlockwiseModules resampling WGCNA
updated 2.3 years ago by ★ 3.0k • written 2.3 years ago by ▴ 30
0
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0
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727
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WGCNA error during network construction
WGCNA Network R
2.6 years ago gitanjali • 0
0
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1
reply
1.5k
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igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 2.7 years ago by 50k • written 5.1 years ago by • 0
0
votes
1
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1.6k
views
Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
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0
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850
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Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.1 years ago martin.schaefer • 0
0
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0
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1.2k
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
3.3 years ago jol.espinoz ▴ 40
15
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17
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23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.4 years ago by ▴ 730 • written 7.6 years ago by ▴ 40
4
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2
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1.1k
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
0
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2
replies
2.1k
views
Soft-threshold in WGCNA
wgcna network bicor threshold
updated 3.7 years ago by ★ 3.0k • written 3.7 years ago by ▴ 80
2
votes
0
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511
views
Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
3.9 years ago hamza_karakurt ▴ 50
5
votes
2
replies
4.1k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by ▴ 30
2
votes
4
replies
1.8k
views
Case-control study using WGCNA
wgcna network rna-seq
4.4 years ago ag1805x ▴ 80
1
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1
reply
1.5k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 10
2
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1
reply
1.4k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
4
votes
3
replies
913
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 5.0 years ago by ★ 3.0k • written 5.0 years ago by ▴ 80
0
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0
replies
796
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Help with creating tumor cell line network
nci network
5.9 years ago torgeirous • 0
0
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0
replies
1.0k
views
Help with generating network from gene expression data
gene expression network cytoscape
6.3 years ago torgeirous • 0
1
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1
reply
1.3k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 6.5 years ago by ▴ 730 • written 6.6 years ago by ▴ 40
1
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1
reply
1.5k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 7.9 years ago by ▴ 120 • written 7.9 years ago by ▴ 660
1
vote
2
replies
1.3k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 7.9 years ago by ▴ 120 • written 7.9 years ago by ▴ 660
0
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2
replies
2.7k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
8.3 years ago hywel.williams • 0
5
votes
14
replies
4.8k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 8.4 years ago by ★ 8.2k • written 8.4 years ago by ▴ 50
0
votes
0
replies
1.2k
views
Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
8.5 years ago kbastard • 0
2
votes
5
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1.4k
views
runing NetBenchmark on my own datasets
software error network
updated 8.5 years ago by ▴ 20 • written 8.6 years ago by ▴ 40
0
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0
replies
1.2k
views
PSICQUIC: Direction of interaction
network protein interaction analysis
8.8 years ago kmezhoud ▴ 10
1
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2
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2.9k
views
cnetplot() - library(clusterProfiler)
clusterProfiler network
8.9 years ago cristina della beffa ▴ 30
0
votes
0
replies
1.5k
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
9.4 years ago Thomas.F.Hahn2 • 0
1
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7
replies
2.7k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
9.5 years ago pshannon ▴ 100
1
vote
2
replies
4.0k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
2
votes
6
replies
4.7k
views
Error running TOMplot in WGCNA package
wgcna network
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
7
votes
1
reply
3.4k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 250
8
votes
4
replies
6.9k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by ▴ 180
0
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0
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1.1k
views
回复： XVector
Network Cancer IRanges XVector
9.6 years ago Hervé Pagès 16k
1
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1
reply
1.4k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 9.8 years ago by ★ 3.0k • written 9.8 years ago by ▴ 130
0
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1
reply
1.6k
views
WGCNA_ problem in creating scale free topology plot
Network Network
updated 9.9 years ago by 65k • written 9.9 years ago by ▴ 130
50 results • Page 1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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