Showing : network • reset
15
votes
17
replies
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
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
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
7
votes
9
replies
3.6k
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
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
5
votes
14
replies
4.7k
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
4
votes
3
replies
897
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
4
votes
2
replies
1.1k
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iSEE - Custom Panel
Network GeneNetwork iSEE
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
3
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2
replies
5.0k
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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
2
votes
6
replies
4.6k
views
Error running TOMplot in WGCNA package
wgcna network
updated 9.6 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
2
votes
4
replies
1.8k
views
Case-control study using WGCNA
wgcna network rna-seq
4.4 years ago ag1805x ▴ 80
2
votes
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
2
votes
1
reply
774
views
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
2
votes
0
replies
501
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Quality Metrics for Graph Clustering for Biological Networks
R protein-interaction networks network
3.9 years ago hamza_karakurt ▴ 50
2
votes
5
replies
1.3k
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runing NetBenchmark on my own datasets
software error network
updated 8.5 years ago by ▴ 20 • written 8.5 years ago by ▴ 40
1
vote
1
reply
1.5k
views
Custom scoring for subnetworks in BioNet
bionet network
updated 7.8 years ago by ▴ 120 • written 7.8 years ago by ▴ 660
1
vote
1
reply
817
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network RCy3
updated 3 months ago by ▴ 20 • written 4 months ago by ▴ 90
1
vote
1
reply
1.5k
views
WGCNA gene clusters vs eigengenes
wgcna network coexpression eigengenes
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 10
1
vote
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 6.5 years ago by ▴ 40
1
vote
2
replies
1.3k
views
Additional high-scoring subnetworks in BioNet
bionet network
updated 7.8 years ago by ▴ 120 • written 7.8 years ago by ▴ 660
1
vote
10
replies
2.0k
views
Interprteting the phylogenomic profiles plot
syntenet synteny Network
written 17 months ago by • 0
1
vote
2
replies
4.0k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna dendrogram network hclust
updated 9.5 years ago by ▴ 180 • written 9.6 years ago by ▴ 250
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
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
1
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2
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2.8k
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cnetplot() - library(clusterProfiler)
clusterProfiler network
8.9 years ago cristina della beffa ▴ 30
0
votes
0
replies
1.1k
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JOB: Biostatistican
Microarray Genetics Proteomics Network Kidney Microarray Genetics Proteomics Network
20.5 years ago Robert Campanell ▴ 10
0
votes
0
replies
1.1k
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[SPAM?] Bioconductor Digest, Vol 41, Issue 22 (Out of Office)
SNP Microarray Annotation GO Network Clustering Survival Cancer hgu133a cdf probe affy
17.8 years ago Todd Nick ▴ 10
0
votes
0
replies
845
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B value cutoff in LIMMA
Network Cancer limma Network Cancer limma
18.0 years ago Gordon Smyth 50k
0
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0
replies
661
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Problem downloading Bioconductor
Network Network
17.9 years ago Seth Falcon ★ 7.4k
0
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0
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642
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Greek characters and subscripts in network graphs
Network Rgraphviz Network Rgraphviz
17.4 years ago Martin Henry H. Stevens ▴ 10
0
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0
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1.1k
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Biocore response to Affymetrix data format changes
Microarray GO Network Cancer cdf affy PROMISE Microarray GO Network Cancer cdf affy
20.8 years ago Kulp, David ▴ 20
0
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0
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1.1k
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Fwd: ASSIST on contrast matrix
Network Homo sapiens limma PROcess Network Homo sapiens limma PROcess
11.7 years ago Seyed Ahmad Mousavi ▴ 10
0
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0
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745
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no connection to biol
Network Network
18.1 years ago Francois Pepin ★ 1.3k
0
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3
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1.9k
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Drawing network graphs (i.e. nodes and edges)
Network Network
updated 18.2 years ago by ▴ 360 • written 18.2 years ago by ▴ 170
0
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0
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1.2k
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Affymetrix Software Development Conference Early Registration rat es - final days
SNP GO Network BEAT SNP GO Network BEAT
21.0 years ago DevNet ▴ 20
0
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0
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652
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need a neural network package for microarray data analysis
Microarray Network Microarray Network
18.4 years ago Stephen Henderson ★ 1.0k
0
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0
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820
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Bug in maNormNN
Microarray Normalization GO Visualization Network nnNorm Microarray Normalization GO
18.4 years ago Tarca, Adi ▴ 570
0
votes
1
reply
906
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Re: Try to run a lots of chips: 32 bits vs 64 bits
Normalization GO Network Normalization GO Network
updated 21.1 years ago by ▴ 530 • written 21.1 years ago by ▴ 430
0
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0
replies
741
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BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building
Microarray Network Microarray Network
11.9 years ago Oliver Ruebenacker ▴ 110
0
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0
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1.3k
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BioC 1.9 is released!
BiocViews SNP Microarray Annotation Normalization Visualization Network Infrastructure SNP
17.6 years ago Seth Falcon ★ 7.4k
0
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0
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897
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help with bayesian network
Network Bayesian Network Bayesian
18.6 years ago goldoni ▴ 10
0
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2
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902
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KEGG analysis
Network Cancer Network Cancer
15.0 years ago Daniel Brewer ★ 1.9k
0
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0
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2.0k
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vacancy postdoc or PhD in the Netherlands
Metabolomics Network Organism Metabolomics Network Organism
15.1 years ago Hendriks, M. ▴ 10
0
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2
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1.2k
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Affymetrix MASv5 code & sample data
Network Network
updated 18.9 years ago by ★ 1.8k • written 18.9 years ago by ▴ 50
0
votes
3
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1.3k
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building enzyme centric metabolic network
Network KEGGSOAP Network KEGGSOAP
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 270
0
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0
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1.9k
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Post Doc position, Berlin Germany
Sequencing Microarray Proteomics Pathways Network Cancer Sequencing Microarray Proteomics
15.0 years ago Paul Hammer ▴ 220
0
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0
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Software Demo for Summer Research Grant
Network Network
14.9 years ago RICHARD SEGALL ▴ 10
0
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0
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1.0k
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bioinformatics programmer position
Network Network
14.8 years ago Wall, Dennis Paul ▴ 80
0
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0
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621
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Invitation to connect on LinkedIn
Network Network
14.7 years ago Lingsheng Dong ▴ 80
0
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Pathview question
Network convert pathview Network convert pathview
10.0 years ago Luo Weijun ★ 1.6k
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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