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Network
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News:
Online course: Network Analysis in Systems Biology with R/Bioconductor
SystemsBiology
Bioconductor
Network
5 months ago
info
▴ 10
0
votes
1
reply
685
views
WGCNA Soft Power
Normalization
DESeq2
Network
RNASeqData
updated 9 months ago by
ATpoint
★ 4.5k • written 9 months ago by
Ömür Koray
• 0
1
vote
1
reply
1.1k
views
How to select subnetworks, or regions, with a certain number of nodes or edges with RCy3
Network
RCy3
updated 10 months ago by
alex.pico
▴ 30 • written 10 months ago by
David R
▴ 90
0
votes
2
replies
665
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData
STRINGdb
DifferentialExpression
GraphAndNetwork
Network
11 months ago • updated 10 months ago
Luca
• 0
0
votes
2
replies
1.5k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 5 months ago by
mariakenneth147
• 0 • written 23 months ago by
pharamac
• 0
1
vote
10
replies
2.5k
views
Interprteting the phylogenomic profiles plot
syntenet
synteny
Network
written 23 months ago by
Alexandros
• 0
0
votes
1
reply
4.3k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network
cluster
WGCNA
RNASeq
updated 15 months ago by
James W. MacDonald
67k • written 15 months ago by
chiwut.wong
• 0
0
votes
0
replies
744
views
News:
Course - Network Analysis in Systems Biology with R/Bioconductor
Bioconductor
Network
RNASeqData
SystemsBiology
16 months ago
info
▴ 10
0
votes
3
replies
752
views
Clustering coefficient of synteny network
Network
syntenet
Clustering
coefficient
16 months ago
Alexandros
• 0
0
votes
0
replies
1.0k
views
WGCNA: minModuleSize is not responding correctly
Network
minModuleSize
WGCNA
wgcna
23 months ago • updated 5 weeks ago
bioinformaticssrm2011
• 0
0
votes
0
replies
944
views
Gene co-expression network analysis with small sample size
Network
2.1 years ago
Senthil
• 0
0
votes
0
replies
660
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
2.1 years ago
Julieta
• 0
2
votes
1
reply
983
views
WGCNA: weird issue of module with a single gene
network
co-expression
WGCNA
updated 2.1 years ago by
andres.firrincieli
▴ 50 • written 2.1 years ago by
ikumar2000
▴ 10
0
votes
1
reply
1.5k
views
WGCNA: Obtaining a consensus network from sampledBlockwiseModules function output
Network
consensus
sampledBlockwiseModules
resampling
WGCNA
updated 2.8 years ago by
Peter Langfelder
★ 3.0k • written 2.8 years ago by
Caleb Bostwick
▴ 30
0
votes
1
reply
1.2k
views
Trouble with gene dendrogram
Network
RNASeq
WGCNA
updated 22 months ago by
shuo
• 0 • written 2.9 years ago by
jms2520
▴ 10
0
votes
0
replies
939
views
WGCNA error during network construction
WGCNA
Network
R
3.1 years ago
gitanjali
• 0
0
votes
1
reply
2.0k
views
Network analysis: Is low confidence score valid (STRING DB)
STRINGdb
Network
updated 3.4 years ago by
Kevin Blighe
★ 4.0k • written 3.4 years ago by
Saransh
• 0
0
votes
0
replies
975
views
Job:
Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks
BiomedicalInformatics
Network
3.6 years ago
martin.schaefer
• 0
0
votes
0
replies
1.4k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network
StatisticalMethod
WGCNA
ExpressionData
3.8 years ago
jol.espinoz
▴ 40
15
votes
17
replies
25k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.9 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.2 years ago by
jol.espinoz
▴ 40
4
votes
2
replies
1.3k
views
iSEE - Custom Panel
Network
GeneNetwork
iSEE
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
Frank
• 0
3
votes
2
replies
6.3k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
updated 2.5 years ago by
annamariabugaj
▴ 10 • written 4.2 years ago by
Arindam
▴ 80
0
votes
2
replies
2.6k
views
Soft-threshold in WGCNA
wgcna
network
bicor
threshold
updated 4.2 years ago by
Peter Langfelder
★ 3.0k • written 4.2 years ago by
Arindam
▴ 80
2
votes
0
replies
638
views
Quality Metrics for Graph Clustering for Biological Networks
R
protein-interaction networks
network
4.4 years ago
hamza_karakurt
▴ 60
5
votes
2
replies
5.2k
views
[WGCNA]How to visualize network of genes in one module
WGCNA
network
updated 4.7 years ago by
Kevin Blighe
★ 4.0k • written 4.8 years ago by
huynguyen96.dnu
▴ 30
2
votes
4
replies
2.2k
views
Case-control study using WGCNA
wgcna
network
rna-seq
4.9 years ago
Arindam
▴ 80
1
vote
1
reply
1.9k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 5.2 years ago by
Gordon Smyth
51k • written 5.2 years ago by
bioming
▴ 10
2
votes
1
reply
1.7k
views
Normalize within-/between-samples RNA-seq counts to weight networks
normalization
CQN
deseq2
RNA-seq
network
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
michael.pierrelee
• 0
4
votes
3
replies
1.1k
views
WGCNA from different lengths RNAseq read
wgcna
network
co-expression
rnaseq
updated 5.5 years ago by
Peter Langfelder
★ 3.0k • written 5.5 years ago by
Arindam
▴ 80
7
votes
9
replies
4.6k
views
WGCNA - networking RNA seq gives only one module!
WGCNA
R
network
co-expression
updated 22 months ago by
Peter Langfelder
★ 3.0k • written 5.5 years ago by
avelarbio46
▴ 10
0
votes
1
reply
1.8k
views
igraph clustering for gene coexpression network
igraph
network
gene corexpression
rna-seq
updated 3.2 years ago by
Gordon Smyth
51k • written 5.6 years ago by
aiswaryabioinfo
• 0
0
votes
0
replies
943
views
Help with creating tumor cell line network
nci
network
6.4 years ago
torgeirous
• 0
0
votes
0
replies
1.2k
views
Help with generating network from gene expression data
gene expression
network
cytoscape
6.8 years ago
torgeirous
• 0
1
vote
1
reply
1.5k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 7.0 years ago by
Lluís Revilla Sancho
▴ 760 • written 7.1 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.7k
views
Custom scoring for subnetworks in BioNet
bionet
network
updated 8.4 years ago by
branislav misovic
▴ 120 • written 8.4 years ago by
enricoferrero
▴ 660
1
vote
2
replies
1.5k
views
Additional high-scoring subnetworks in BioNet
bionet
network
updated 8.4 years ago by
branislav misovic
▴ 120 • written 8.4 years ago by
enricoferrero
▴ 660
0
votes
2
replies
2.9k
views
WGCNA - Using real data for tutorial III
pathways
wgcna
network
rna-seq
8.8 years ago
hywel.williams
• 0
5
votes
14
replies
5.2k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape
r
network
graphBAM object
updated 8.9 years ago by
Dan Tenenbaum
★ 8.2k • written 8.9 years ago by
alptaciroglu
▴ 50
0
votes
0
replies
1.3k
views
Job:
Post-doc: Bioinformatics/Metabolic networks (Genoscope, near Paris, France)
network
metabolism
post-doc
Job
9.0 years ago
kbastard
• 0
2
votes
5
replies
1.5k
views
runing NetBenchmark on my own datasets
software error
network
updated 9.1 years ago by
pau.bellot
▴ 20 • written 9.1 years ago by
Angel
▴ 40
0
votes
0
replies
1.4k
views
PSICQUIC: Direction of interaction
network
protein interaction analysis
9.3 years ago
kmezhoud
▴ 10
1
vote
2
replies
3.2k
views
cnetplot() - library(clusterProfiler)
clusterProfiler
network
9.4 years ago
cristina della beffa
▴ 30
0
votes
0
replies
1.6k
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
9.9 years ago
Thomas.F.Hahn2
• 0
1
vote
7
replies
3.0k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny
network
interactions
10.0 years ago
pshannon
▴ 100
1
vote
2
replies
4.3k
views
Rearrange dendrogram to match merged modules in WGCNA?
wgcna
dendrogram
network
hclust
updated 10.1 years ago by
Keith Hughitt
▴ 180 • written 10.1 years ago by
Jon Bråte
▴ 260
2
votes
6
replies
5.1k
views
Error running TOMplot in WGCNA package
wgcna
network
updated 10.1 years ago by
Keith Hughitt
▴ 180 • written 10.1 years ago by
Jon Bråte
▴ 260
7
votes
1
reply
3.7k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq
network
limma
updated 10.1 years ago by
Steve Lianoglou
★ 13k • written 10.1 years ago by
Jon Bråte
▴ 260
8
votes
4
replies
7.4k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna
plotDendroAndColors
Network
updated 10.2 years ago by
Peter Langfelder
★ 3.0k • written 10.2 years ago by
Keith Hughitt
▴ 180
0
votes
0
replies
1.2k
views
回复: XVector
Network
Cancer
IRanges
XVector
10.2 years ago
Hervé Pagès
16k
1
vote
1
reply
1.5k
views
WGCNA_ Eigengene and sample complications correlations
Network
Network
updated 10.4 years ago by
Peter Langfelder
★ 3.0k • written 10.4 years ago by
amit kumar subudhi
▴ 130
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Comment: BiomaRt Possible Ensembl SSL connectivity problems detected.
by
Adam
• 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Comment: Problem at champ.load
by
icecreamlover
• 0
Hello! Were you able to figure this out? I am running into the same error!
Comment: ChAMP - obtaining beta values using EPICv2 annotation
by
icecreamlover
• 0
Hello, Were you able to fix the error? I used the same document and I am running into the same error. I am curious if you have any feedba…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected.
by
Adam
• 0
Can this please be revisited and corrected ASAP? I'm encountering the same issue, using a slightly more modern version of R (4.1.0). It s…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Thank you!
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shepherl
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