Showing : network • reset
0
votes
1
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331
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
vote
1
reply
860
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 5 months ago by ▴ 90
0
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2
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373
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
0
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2
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946
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 2 days ago by • 0 • written 17 months ago by • 0
1
vote
10
replies
2.1k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 18 months ago by • 0
0
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1
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2.1k
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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561
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
10 months ago info ▴ 10
0
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3
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591
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
10 months ago Alexandros • 0
0
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0
replies
786
views
WGCNA: minModuleSize is not responding correctly
wgcna Network WGCNA minModuleSize
18 months ago • updated 17 months ago bioinformaticssrm2011 • 0
0
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0
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761
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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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536
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
20 months ago Julieta • 0
2
votes
1
reply
811
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WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 20 months ago by ▴ 50 • written 20 months ago by ▴ 10
0
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1
reply
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 2.4 years ago by ▴ 30
0
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1
reply
983
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 16 months ago by • 0 • written 2.5 years ago by ▴ 10
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0
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750
views
WGCNA error during network construction
WGCNA Network R
2.6 years ago gitanjali • 0
0
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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
0
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0
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857
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.1 years ago martin.schaefer • 0
0
votes
0
replies
1.2k
views
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
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.5 years ago by ▴ 730 • written 7.7 years ago by ▴ 40
4
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2
replies
1.1k
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
3
votes
2
replies
5.1k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 24 months ago by ▴ 10 • written 3.8 years ago by ▴ 80
0
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2
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2.2k
views
Soft-threshold in WGCNA
wgcna network bicor threshold
updated 3.8 years ago by ★ 3.0k • written 3.8 years ago by ▴ 80
2
votes
0
replies
517
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
4.2k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 4.3 years ago by ★ 3.9k • written 4.3 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
vote
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
votes
1
reply
1.5k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
4
votes
3
replies
927
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
7
votes
9
replies
3.7k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 16 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
0
votes
1
reply
1.5k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 2.8 years ago by 50k • written 5.1 years ago by • 0
0
votes
0
replies
802
views
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 6.6 years ago by ▴ 730 • written 6.6 years ago by ▴ 40
1
vote
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
replies
1.4k
views
runing NetBenchmark on my own datasets
software error network
updated 8.6 years ago by ▴ 20 • written 8.6 years ago by ▴ 40
0
votes
0
replies
1.2k
views
PSICQUIC: Direction of interaction
network protein interaction analysis
8.9 years ago kmezhoud ▴ 10
1
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2
replies
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
vote
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
3.5k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 250
8
votes
4
replies
7.0k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 9.7 years ago by ★ 3.0k • written 9.7 years ago by ▴ 180
0
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0
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1.1k
views
回复： XVector
Network Cancer IRanges XVector
9.7 years ago Hervé Pagès 16k
1
vote
1
reply
1.4k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 9.9 years ago by ★ 3.0k • written 9.9 years ago by ▴ 130
0
votes
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
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Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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