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network
•
reset
0
votes
10
replies
1.9k
views
assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Microarray
Annotation
GO
Network
Regression
Survival
Infrastructure
Escherichia coli
ROC
10.2 years ago
Julie Zhu
★ 4.3k
0
votes
7
replies
1.4k
views
Kegg pathway --> gene network
Pathways
Network
Pathways
Network
updated 14.4 years ago by
Martin Morgan
25k • written 14.5 years ago by
Gavai, Anand
▴ 40
1
vote
10
replies
831
views
Interprteting the phylogenomic profiles plot
syntenet
synteny
Network
updated 24 days ago by
Rico
• 0 • written 6 months ago by
Alexandros
• 0
0
votes
12
replies
1.7k
views
new package for generating interactive HTML reports
Network
limma
GOstats
GSEAlm
edgeR
ReportingTools
Network
limma
GOstats
GSEAlm
edgeR
updated 10.4 years ago by
Malcolm Cook
★ 1.6k • written 10.4 years ago by
Josh Kaminker
▴ 20
1
vote
7
replies
2.3k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny
network
interactions
8.6 years ago
pshannon
▴ 100
0
votes
3
replies
1.1k
views
tool for drawing interaction network
Pathways
Network
Pathways
Network
updated 13.0 years ago by
Michael Imbeault
▴ 220 • written 13.0 years ago by
Guido Hooiveld
★ 3.6k
0
votes
3
replies
1.5k
views
identifying network communities in a protein-protein interaction graph
Network
Network
updated 13.4 years ago by
Stijn van Dongen
▴ 80 • written 13.4 years ago by
Coghlan, Avril
▴ 190
0
votes
2
replies
1.1k
views
limma for homemade microarray - question on NAs and multiple probes for one gene
Microarray
Normalization
GO
Network
Cancer
probe
limma
Microarray
Normalization
GO
probe
updated 9.9 years ago by
Gordon Smyth
47k • written 9.9 years ago by
Peter Langfelder
★ 2.8k
0
votes
3
replies
1.9k
views
WGCNA chooseTopHubInEachModule function
Network
Network
10.9 years ago
Sudeep Sahadevan
▴ 20
0
votes
7
replies
871
views
(no subject)
Network
Network
updated 10.1 years ago by
Gordon Smyth
47k • written 10.1 years ago by
abdul rawoof
▴ 60
0
votes
2
replies
852
views
Error in gammaFitEM for library(lumi) [Possible Bug]
Preprocessing
Network
Preprocessing
Network
updated 11.3 years ago by
Pan Du
▴ 440 • written 11.3 years ago by
Chang Jun Park
▴ 10
0
votes
3
replies
1.6k
views
Drawing network graphs (i.e. nodes and edges)
Network
Network
updated 17.3 years ago by
Saurin D. Jani
▴ 360 • written 17.3 years ago by
Peter
▴ 170
0
votes
2
replies
5.1k
views
WGCNA package
Network
Network
updated 9.1 years ago by
Peter Langfelder
★ 2.8k • written 9.1 years ago by
amit kumar subudhi
▴ 130
8
votes
4
replies
6.0k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna
plotDendroAndColors
Network
updated 8.7 years ago by
Peter Langfelder
★ 2.8k • written 8.7 years ago by
Keith Hughitt
▴ 180
0
votes
2
replies
1.1k
views
proposed: a bridge between R and Cytoscape
Visualization
Network
graph
Visualization
Network
graph
updated 12.9 years ago by
Steve Lianoglou
13k • written 12.9 years ago by
Paul Shannon
★ 1.1k
0
votes
2
replies
795
views
Network plot
Network
Network
updated 12.9 years ago by
Sean Davis
21k • written 12.9 years ago by
Hernando Martínez
▴ 100
15
votes
17
replies
19k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 2.5 years ago by
Lluís Revilla Sancho
▴ 710 • written 6.7 years ago by
jol.espinoz
▴ 40
0
votes
7
replies
1.2k
views
GeneAnswer package Query
Network
graph
Network
graph
updated 10.7 years ago by
Gilbert Feng
▴ 300 • written 10.7 years ago by
Reema Singh
▴ 570
0
votes
3
replies
1.1k
views
building enzyme centric metabolic network
Network
KEGGSOAP
Network
KEGGSOAP
updated 14.1 years ago by
Martin Morgan
25k • written 14.1 years ago by
anupam sinha
▴ 270
0
votes
4
replies
1.2k
views
Bioconductor 2.8 is released
SNP
Sequencing
miRNA
Microarray
Annotation
Normalization
Pathways
Preprocessing
Network
updated 12.1 years ago by
Ivan Gregoretti
▴ 310 • written 12.1 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
2
replies
1.1k
views
AgiMicroRna package is not available at bioconductor or not in active form???
Microarray
Network
microRNA
AgiMicroRna
Microarray
Network
microRNA
AgiMicroRna
updated 13.2 years ago by
Alberto Goldoni
▴ 60 • written 13.2 years ago by
Sean Davis
21k
2
votes
6
replies
4.0k
views
Error running TOMplot in WGCNA package
wgcna
network
updated 8.7 years ago by
Keith Hughitt
▴ 180 • written 8.7 years ago by
Jon Bråte
▴ 240
0
votes
2
replies
2.3k
views
WGCNA - Using real data for tutorial III
pathways
wgcna
network
rna-seq
7.4 years ago
hywel.williams
• 0
0
votes
8
replies
1.4k
views
Visualization of metabolic network in lpSolve format
Network
Network
10.2 years ago
Denis Kazakiewicz
▴ 70
0
votes
4
replies
1.1k
views
Example of converting graphNEL object to ajacency matrix?
Network
convert
Network
convert
updated 15.1 years ago by
rgentleman
★ 5.5k • written 15.1 years ago by
Zembower, Kevin
▴ 50
1
vote
1
reply
1.2k
views
WGCNA_ Eigengene and sample complications correlations
Network
Network
updated 8.9 years ago by
Peter Langfelder
★ 2.8k • written 8.9 years ago by
amit kumar subudhi
▴ 130
0
votes
1
reply
1.5k
views
How to compare GO term lists and create matching network?
GO
Network
GUI
Organism
GO
Network
GUI
Organism
updated 9.5 years ago by
Paul Shannon
▴ 750 • written 9.6 years ago by
biotech
▴ 160
0
votes
2
replies
3.5k
views
Gene filtering for RNA-seq data
Normalization
GO
Network
HTSFilter
DESeq2
Normalization
GO
Network
HTSFilter
DESeq2
updated 9.5 years ago by
Michael Love
40k • written 9.5 years ago by
Guest User
★ 12k
0
votes
1
reply
900
views
5000 nodes RCytoscape
Network
graph
Network
graph
10.2 years ago
Paul Shannon
▴ 750
0
votes
1
reply
1.3k
views
WGCNA_ problem in creating scale free topology plot
Network
Network
updated 8.9 years ago by
James W. MacDonald
62k • written 8.9 years ago by
amit kumar subudhi
▴ 130
0
votes
1
reply
668
views
Connect with me on LinkedIn
Network
Network
10.6 years ago
gabriel teku
▴ 80
0
votes
1
reply
773
views
Re: Try to run a lots of chips: 32 bits vs 64 bits
Normalization
GO
Network
Normalization
GO
Network
updated 20.2 years ago by
Anthony Rossini
▴ 530 • written 20.2 years ago by
Nicholas Lewin-Koh
▴ 430
0
votes
3
replies
845
views
rna-seq
Microarray
Pathways
Network
goseq
Microarray
Pathways
Network
goseq
updated 10.7 years ago by
Aliaksei Holik
▴ 350 • written 10.7 years ago by
Guest User
★ 12k
7
votes
1
reply
3.1k
views
Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
rnaseq
network
limma
updated 8.7 years ago by
Steve Lianoglou
13k • written 8.7 years ago by
Jon Bråte
▴ 240
0
votes
1
reply
974
views
FrozenRMA how to
Microarray
Network
hgu133plus2
Biobase
PROcess
KEGGSOAP
beadarray
EBImage
edgeR
frma
updated 11.2 years ago by
Matthew McCall
▴ 830 • written 11.2 years ago by
Alex Sanchez
▴ 20
0
votes
2
replies
1.1k
views
bug in rendering reciprocal edges?
Network
graph
Rgraphviz
Network
graph
Rgraphviz
updated 11.8 years ago by
Nishant Gopalakrishnan
▴ 340 • written 11.8 years ago by
Wouter van Atteveldt
▴ 20
0
votes
5
replies
3.1k
views
Adjacency to network using R
Visualization
Network
convert
Visualization
Network
convert
updated 11.2 years ago by
Tim Triche
★ 4.2k • written 11.2 years ago by
pankaj borah
▴ 120
0
votes
1
reply
1.2k
views
Which resources for pathway analysis?
Pathways
Network
SPIA
DEGraph
Pathways
Network
SPIA
DEGraph
updated 12.3 years ago by
January Weiner
▴ 370 • written 12.3 years ago by
laurent jacob
▴ 100
0
votes
1
reply
1.2k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq
GO
Network
rtracklayer
CAMERA
chipseq
Gviz
ChIPSeq
GO
Network
rtracklayer
Gviz
updated 9.6 years ago by
Michael Lawrence
11k • written 9.6 years ago by
Miles Pufall
▴ 40
0
votes
4
replies
1.2k
views
[R] RCytoscape setPosition error
Network
Cancer
graph
Network
Cancer
graph
updated 12.3 years ago by
Fahim Md
▴ 250 • written 12.3 years ago by
Paul Shannon
★ 1.1k
0
votes
2
replies
1.2k
views
RV: wgcna
Network
Cancer
Network
Cancer
updated 11.9 years ago by
Robert Castelo
★ 3.0k • written 11.9 years ago by
Raquel Martinez Garcia
▴ 50
0
votes
1
reply
706
views
network analyses on genes or probesets
Microarray
Annotation
Normalization
Preprocessing
Network
Microarray
Annotation
Network
updated 14.2 years ago by
Marc Carlson
★ 7.2k • written 14.2 years ago by
Markus Schmidberger
▴ 380
0
votes
2
replies
1.0k
views
Affymetrix MASv5 code & sample data
Network
Network
updated 18.0 years ago by
Adaikalavan Ramasamy
★ 1.8k • written 18.0 years ago by
Lelivelt, Mike
▴ 50
0
votes
2
replies
752
views
KEGG analysis
Network
Cancer
Network
Cancer
14.2 years ago
Daniel Brewer
★ 1.9k
0
votes
1
reply
600
views
BioPAX/SBPAX import for MicroArray Analysis and Hypothesis Building
Microarray
Pathways
Network
Microarray
Pathways
Network
updated 11.0 years ago by
Tim Triche
★ 4.2k • written 11.0 years ago by
Oliver Ruebenacker
▴ 110
0
votes
6
replies
1.2k
views
Network install of packages
Network
Network
updated 14.6 years ago by
Sean Davis
21k • written 14.6 years ago by
Anthony Mullen
▴ 20
0
votes
1
reply
1.2k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP
Coverage
Network
Cancer
TranscriptDb
IRanges
RCytoscape
ggbio
Gviz
SNP
Coverage
updated 11.1 years ago by
Tim Triche
★ 4.2k • written 11.1 years ago by
Ekta Jain
▴ 370
0
votes
1
reply
918
views
Unable to
Network
Network
updated 10.3 years ago by
Dan Tenenbaum
★ 8.2k • written 10.3 years ago by
Guest User
★ 12k
0
votes
1
reply
703
views
Aniket Mishra wants to stay in touch on LinkedIn
Network
Network
12.6 years ago
Aniket Vatsya
▴ 40
0
votes
6
replies
1.1k
views
Regarding KEGGgraph
Pathways
Network
PROcess
Pathways
Network
PROcess
updated 13.4 years ago by
Wolfgang Huber
13k • written 13.4 years ago by
anupam sinha
▴ 270
50 results • Page
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Replies
Comment: Installing densvis on a Singularity container
by
alan.ocallaghan
▴ 120
Do you have gfortran installed? eg [this installation package][1] [1]: https://github.com/fxcoudert/gfortran-for-macOS
Comment: Installing densvis on a Singularity container
by
azp0136
• 0
I get the same error when I try to install densvis in R with `BiocManager::install("densvis")` and I have no idea how to solve this problem…
Comment: Error in DGEList(counts = cnt, group = group) : non-numeric values found in c
by
Luis
• 0
Thank you so much!
Comment: Error in DGEList(counts = cnt, group = group) : non-numeric values found in c
by
Luis
• 0
I understand, thank you very much for all the support and collaboration!
Answer: Normalized counts from LRT or Wald test?
by
ATpoint
★ 2.8k
If the same samples are present in the object then the normalized counts are exactly the same independent of the design or test you use.
Votes
Comment: Visualization of negative log CPM values
Answer: Extracting fitted expression matrix from Limma
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Comment: Visualization of negative log CPM values
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
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