Showing : Network • reset
3
votes
4
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7.9k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.2 years ago by ▴ 80
0
votes
0
replies
613
views
News: Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology Bioconductor Network
17 months ago info ▴ 10
0
votes
1
reply
1.1k
views
WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
vote
1
reply
1.5k
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 21 months ago by ▴ 30 • written 22 months ago by ▴ 90
0
votes
2
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1.1k
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
22 months ago Luca • 0
0
votes
2
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2.4k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 17 months ago by • 0 • written 2.9 years ago by • 0
1
vote
10
replies
3.0k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 2.9 years ago by • 0
0
votes
1
reply
5.1k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
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0
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1.0k
views
News: Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor Network RNASeqData SystemsBiology
2.3 years ago info ▴ 10
0
votes
3
replies
1.2k
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
2.3 years ago Alexandros • 0
0
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0
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1.4k
views
WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.9 years ago • updated 13 months ago bioinformaticssrm2011 • 0
0
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0
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1.2k
views
Gene co-expression network analysis with small sample size
Network
3.0 years ago Senthil • 0
0
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0
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1.1k
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
3.1 years ago Julieta • 0
2
votes
1
reply
1.2k
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 3.1 years ago by ▴ 50 • written 3.1 years ago by ▴ 10
0
votes
1
reply
1.9k
views
WGCNA: Obtaining a consensus network from sampledBlockwiseModules function output
Network consensus sampledBlockwiseModules resampling WGCNA
updated 3.7 years ago by ★ 3.0k • written 3.8 years ago by ▴ 30
0
votes
1
reply
1.4k
views
Trouble with gene dendrogram
Network RNASeq WGCNA
updated 2.8 years ago by • 0 • written 3.9 years ago by ▴ 10
0
votes
0
replies
1.2k
views
WGCNA error during network construction
WGCNA Network R
4.1 years ago gitanjali • 0
0
votes
1
reply
3.0k
views
Network analysis: Is low confidence score valid (STRING DB)
STRINGdb Network
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
0
votes
0
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1.2k
views
Job: Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks BiomedicalInformatics Network
4.6 years ago martin.schaefer • 0
0
votes
0
replies
1.7k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.8 years ago jol.espinoz ▴ 40
15
votes
17
replies
30k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 4.9 years ago by ▴ 760 • written 9.1 years ago by ▴ 40
4
votes
2
replies
1.6k
views
iSEE - Custom Panel
Network GeneNetwork iSEE
updated 5.0 years ago by ★ 29k • written 5.0 years ago by • 0
0
votes
2
replies
3.1k
views
Soft-threshold in WGCNA
wgcna network bicor threshold
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 80
2
votes
0
replies
822
views
Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
5.4 years ago hamza_karakurt ▴ 60
5
votes
2
replies
6.8k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 5.7 years ago by ★ 4.0k • written 5.7 years ago by ▴ 30
2
votes
4
replies
2.7k
views
Case-control study using WGCNA
wgcna network rna-seq
5.9 years ago Arindam ▴ 80
1
vote
1
reply
2.4k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 10
2
votes
1
reply
2.1k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization CQN deseq2 RNA-seq network
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
4
votes
3
replies
1.4k
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 6.5 years ago by ★ 3.0k • written 6.5 years ago by ▴ 80
7
votes
9
replies
6.1k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 2.8 years ago by ★ 3.0k • written 6.5 years ago by ▴ 10
0
votes
1
reply
2.1k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 4.2 years ago by 53k • written 6.6 years ago by • 0
0
votes
0
replies
1.2k
views
Help with creating tumor cell line network
nci network
7.4 years ago torgeirous • 0
0
votes
0
replies
1.5k
views
Help with generating network from gene expression data
gene expression network cytoscape
7.8 years ago torgeirous • 0
1
vote
1
reply
1.8k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 8.0 years ago by ▴ 760 • written 8.0 years ago by ▴ 40
1
vote
1
reply
1.9k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 9.4 years ago by ▴ 120 • written 9.4 years ago by ▴ 680
1
vote
2
replies
1.8k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 9.4 years ago by ▴ 120 • written 9.4 years ago by ▴ 680
0
votes
2
replies
3.3k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.8 years ago hywel.williams • 0
5
votes
14
replies
6.0k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 9.9 years ago by ★ 8.2k • written 9.9 years ago by ▴ 50
0
votes
0
replies
1.5k
views
Job: Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network metabolism post-doc Job
10.0 years ago kbastard • 0
2
votes
5
replies
1.9k
views
runing NetBenchmark on my own datasets
software error network
updated 10.0 years ago by ▴ 20 • written 10.0 years ago by ▴ 40
0
votes
0
replies
1.6k
views
PSICQUIC: Direction of interaction
network protein interaction analysis
10.3 years ago kmezhoud ▴ 10
1
vote
2
replies
3.6k
views
cnetplot() - library(clusterProfiler)
clusterProfiler network
10.4 years ago cristina della beffa ▴ 30
0
votes
0
replies
1.8k
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
10.8 years ago Thomas.F.Hahn2 • 0
1
vote
7
replies
3.4k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
11.0 years ago pshannon ▴ 100
1
vote
2
replies
4.7k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 11.0 years ago by ▴ 180 • written 11.1 years ago by ▴ 270
2
votes
6
replies
5.7k
views
Error running TOMplot in WGCNA package
wgcna network
updated 11.1 years ago by ▴ 180 • written 11.1 years ago by ▴ 270
7
votes
1
reply
4.1k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq network limma
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ▴ 270
8
votes
4
replies
8.1k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 11.1 years ago by ★ 3.0k • written 11.1 years ago by ▴ 180
0
votes
0
replies
1.4k
views
回复： XVector
Network Cancer IRanges XVector
11.1 years ago Hervé Pagès 16k
1
vote
1
reply
1.7k
views
WGCNA_ Eigengene and sample complications correlations
Network Network
updated 11.3 years ago by ★ 3.0k • written 11.3 years ago by ▴ 130
180 results • Page 1 of 4
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
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