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
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1
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884
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 13 months ago by ★ 4.7k • written 13 months ago by • 0
1
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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 14 months ago by ▴ 30 • written 15 months ago by ▴ 90
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2
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876
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
15 months ago Luca • 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 10 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
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4.8k
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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 19 months ago by 68k • written 19 months ago by • 0
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868
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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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986
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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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1.1k
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Gene co-expression network analysis with small sample size
Network
2.4 years ago Senthil • 0
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756
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
2.5 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 2.2 years ago by • 0 • written 3.3 years ago by ▴ 10
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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
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Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
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1.1k
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Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
4.0 years ago martin.schaefer • 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
4.2 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 4.3 years ago by ▴ 760 • written 8.5 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 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
3
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2
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6.9k
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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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714
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Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
4.8 years ago hamza_karakurt ▴ 60
5
votes
2
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5.9k
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
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2.4k
views
Case-control study using WGCNA
wgcna network rna-seq
5.3 years ago Arindam ▴ 80
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1
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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
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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
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3
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1.2k
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 5.9 years ago by ★ 3.0k • written 5.9 years ago by ▴ 80
7
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9
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5.2k
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WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.2 years ago by ★ 3.0k • written 5.9 years ago by ▴ 10
0
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1
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1.9k
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igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 3.6 years ago by 52k • written 6.0 years ago by • 0
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0
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1.0k
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Help with creating tumor cell line network
nci network
6.8 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
7.2 years ago torgeirous • 0
1
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1
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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
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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
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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
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2
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3.0k
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WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.2 years ago hywel.williams • 0
5
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14
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5.5k
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Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 9.3 years ago by ★ 8.2k • written 9.3 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
9.4 years ago kbastard • 0
2
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5
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1.6k
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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
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1.5k
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PSICQUIC: Direction of interaction
network protein interaction analysis
9.7 years ago kmezhoud ▴ 10
1
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2
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3.4k
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cnetplot() - library(clusterProfiler)
clusterProfiler network
9.8 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
10.2 years ago Thomas.F.Hahn2 • 0
1
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3.1k
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Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.4 years ago pshannon ▴ 100
1
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2
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4.5k
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Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 10.4 years ago by ▴ 180 • written 10.5 years ago by ▴ 260
2
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6
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5.4k
views
Error running TOMplot in WGCNA package
wgcna network
updated 10.5 years ago by ▴ 180 • written 10.5 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 10.5 years ago by ★ 13k • written 10.5 years ago by ▴ 260
8
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4
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7.7k
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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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1.3k
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回复： XVector
Network Cancer IRanges XVector
10.5 years ago Hervé Pagès 16k
1
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1
reply
1.6k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 10.7 years ago by ★ 3.0k • written 10.7 years ago by ▴ 130
50 results • Page 1 of 1
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
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Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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