Showing : network • reset
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News: Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology Bioconductor Network
9 months ago info ▴ 10
0
votes
1
reply
865
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 13 months ago by ★ 4.7k • written 13 months ago by • 0
1
vote
1
reply
1.3k
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 14 months ago by ▴ 30 • written 14 months ago by ▴ 90
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2
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856
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
14 months ago Luca • 0
0
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2
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1.9k
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 9 months ago by • 0 • written 2.3 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 2.3 years ago by • 0
0
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1
reply
4.8k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
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856
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News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
20 months ago info ▴ 10
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3
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964
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
20 months ago Alexandros • 0
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1.2k
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WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.3 years ago • updated 5 months ago bioinformaticssrm2011 • 0
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1.0k
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Gene co-expression network analysis with small sample size
Network
2.4 years ago Senthil • 0
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744
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
2.4 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 2.5 years ago by ▴ 50 • written 2.5 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 3.1 years ago by ★ 3.0k • written 3.2 years ago by ▴ 30
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1
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1.3k
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Trouble with gene dendrogram
Network RNASeq WGCNA
updated 2.1 years ago by • 0 • written 3.3 years ago by ▴ 10
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0
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1.1k
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WGCNA error during network construction
WGCNA Network R
3.4 years ago gitanjali • 0
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1
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2.4k
views
Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
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0
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1.1k
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Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
3.9 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
4.1 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 4.2 years ago by ▴ 760 • written 8.5 years ago by ▴ 40
4
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2
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1.4k
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
3
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2
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6.8k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 2.8 years ago by ▴ 10 • written 4.6 years ago by ▴ 80
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2
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2.8k
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Soft-threshold in WGCNA
wgcna network bicor threshold
updated 4.6 years ago by ★ 3.0k • written 4.6 years ago by ▴ 80
2
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0
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707
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Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
4.7 years ago hamza_karakurt ▴ 60
5
votes
2
replies
5.8k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 30
2
votes
4
replies
2.4k
views
Case-control study using WGCNA
wgcna network rna-seq
5.2 years ago Arindam ▴ 80
1
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1
reply
2.1k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 10
2
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1
reply
1.9k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
4
votes
3
replies
1.2k
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 80
7
votes
9
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5.2k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.1 years ago by ★ 3.0k • written 5.8 years ago by ▴ 10
0
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1
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1.9k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 3.6 years ago by 52k • written 5.9 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
6.7 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
7.1 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 7.4 years ago by ▴ 760 • written 7.4 years ago by ▴ 40
1
vote
1
reply
1.8k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 8.7 years ago by ▴ 120 • written 8.7 years ago by ▴ 680
1
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2
replies
1.6k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 8.7 years ago by ▴ 120 • written 8.7 years ago by ▴ 680
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
9.1 years ago hywel.williams • 0
5
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14
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5.5k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 9.2 years ago by ★ 8.2k • written 9.2 years ago by ▴ 50
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0
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1.4k
views
Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
9.3 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 9.4 years ago by ▴ 20 • written 9.4 years ago by ▴ 40
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0
replies
1.5k
views
PSICQUIC: Direction of interaction
network protein interaction analysis
9.6 years ago kmezhoud ▴ 10
1
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2
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3.4k
views
cnetplot() - library(clusterProfiler)
clusterProfiler network
9.7 years ago cristina della beffa ▴ 30
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0
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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
10.2 years ago Thomas.F.Hahn2 • 0
1
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7
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3.1k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.3 years ago pshannon ▴ 100
1
vote
2
replies
4.5k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 10.4 years ago by ▴ 180 • written 10.4 years ago by ▴ 260
2
votes
6
replies
5.3k
views
Error running TOMplot in WGCNA package
wgcna network
updated 10.4 years ago by ▴ 180 • written 10.4 years ago by ▴ 260
7
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1
reply
3.9k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 10.4 years ago by ★ 13k • written 10.4 years ago by ▴ 260
8
votes
4
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7.6k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 10.5 years ago by ★ 3.0k • written 10.5 years ago by ▴ 180
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0
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1.3k
views
回复： XVector
Network Cancer IRanges XVector
10.5 years ago Hervé Pagès 16k
1
vote
1
reply
1.6k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 10.7 years ago by ★ 3.0k • written 10.7 years ago by ▴ 130
50 results • Page 1 of 1
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Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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