Showing : graph • reset
0
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1
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244
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Representation of self-loops and the calculation of degrees
graph
updated 10 weeks ago by 6.6k • written 5 months ago by • 0
2
votes
4
replies
3.6k
views
Unable to upload an App in shinyapps.io with bioconductor packages
shinny graph RBGL
updated 9 weeks ago by ▴ 10 • written 2.3 years ago by • 0
0
votes
1
reply
601
views
maSigPro see.genes expression profile graphs. Change color and label text size
maSigPro graph
updated 2.5 years ago by ▴ 90 • written 2.5 years ago by • 0
3
votes
3
replies
1.1k
views
Can't install graph package
graph
updated 3.1 years ago by 25k • written 3.1 years ago by ▴ 10
1
vote
2
replies
706
views
Library for Node Influence package
Graph gene regulatory network node influence gene ranking
updated 3.5 years ago by 3.8k • written 3.5 years ago by ▴ 50
0
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0
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730
views
igraph PoTRA error
graph pathways igraph
5.2 years ago genomic8328 ▴ 10
1
vote
4
replies
1.6k
views
How do I convert kegg info on drug to a format allowing me to calculate similarities?
keggrest chemminer fmcsr graph
written 5.2 years ago by • 0
2
votes
1
reply
1.5k
views
Pathview graph with multiple states/samples or time series
Pathways graph Pathways graph
updated 5.3 years ago by • 0 • written 9.7 years ago by ★ 1.6k
1
vote
1
reply
762
views
How to get the list of the components of all containers from the active RedeR session?
reder graph
updated 5.6 years ago by ▴ 10 • written 5.7 years ago by ▴ 10
0
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1
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787
views
CRISPRseek How to get a correct result of searchHits2 ?
crisprseek graph
updated 5.9 years ago by ★ 4.3k • written 5.9 years ago by • 0
0
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1
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1.0k
views
Visualizing Linear Model Coefficients in R
R deseq2 graph linear model
updated 6.0 years ago by 40k • written 6.0 years ago by • 0
2
votes
3
replies
2.7k
views
How to convert graphNEL object into Adjacency Matrix?
graph kegggraph xml
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by • 0
2
votes
2
replies
1.8k
views
Best practices for converting adj matrix -> graphNEL
graph adjacency matrix
6.5 years ago bryon ▴ 10
1
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1
reply
773
views
Fastest way to get the distances between pairs of graph nodes
graph rgbl dag
updated 6.5 years ago by 13k • written 6.5 years ago by ▴ 110
0
votes
1
reply
908
views
ChIPseeker plotAvgProf2: order of panels
graph
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by ▴ 30
0
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1
reply
1.7k
views
Gviz Sashimi Plot height/colour/count
graph gviz
updated 6.7 years ago by ▴ 730 • written 7.0 years ago by ▴ 10
0
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1
reply
856
views
plot pdf error
graph
updated 7.2 years ago by ▴ 990 • written 7.2 years ago by • 0
3
votes
2
replies
2.1k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna rbgl graph coexpression hub genes
updated 7.2 years ago by ★ 2.8k • written 7.2 years ago by ▴ 150
1
vote
1
reply
1.1k
views
Rgraphviz and margins
graph Rgraphviz graph Rgraphviz
updated 7.4 years ago by • 0 • written 11.9 years ago by ▴ 80
0
votes
2
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1.6k
views
cummRbund MDSplot error
software error graph R cummerbund
updated 7.5 years ago by • 0 • written 7.5 years ago by • 0
2
votes
2
replies
1.5k
views
Ploting with NA values in Gviz (generic function from plot)
Gviz Plot NA graph Job
updated 7.9 years ago by 63k • written 7.9 years ago by ▴ 40
0
votes
1
reply
913
views
Graph isomorphism in Rcytoscape
graph isomorphism in Rcytoscape
updated 7.9 years ago by ▴ 760 • written 7.9 years ago by • 0
0
votes
1
reply
1.7k
views
Graph viewer for Reactome Pathways
bioconductor package reactome graph
updated 8.0 years ago by ★ 2.0k • written 8.0 years ago by ▴ 10
0
votes
5
replies
1.6k
views
R plot error
r bioconductor graph plot data representation in graphical forms
8.0 years ago megha.24may • 0
0
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2
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1.6k
views
How to specifiy colors for polygon links when using circos function of OmicCircos package
graph omiccircos
updated 8.3 years ago by ▴ 50 • written 8.3 years ago by • 0
0
votes
4
replies
3.2k
views
R graphs: all paths lengths between two nodes in a directed graph
graph graph
updated 8.3 years ago by • 0 • written 14.1 years ago by ▴ 20
2
votes
2
replies
1.7k
views
GO offspring consistency
annotation GO graph gene ontology
updated 8.5 years ago by 1.6k • written 8.5 years ago by • 0
0
votes
3
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1.3k
views
generating graph with different rown ames and column names
graph rgraphviz
updated 8.6 years ago by 16k • written 8.6 years ago by • 0
0
votes
4
replies
1.9k
views
Error for plotDEXSeq and warning for estimateDispersions
graph DEXSeq
updated 8.7 years ago by ★ 1.8k • written 8.7 years ago by ▴ 20
0
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1
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1.3k
views
Problem in K- means clustering
hgu133plus2 graph hgu133plus2 graph
updated 8.8 years ago by ▴ 380 • written 8.8 years ago by ▴ 10
0
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0
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834
views
bug in graph::removeEdge() on UGs with graphBAM objects
graph graph
8.8 years ago Robert Castelo ★ 3.0k
0
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1
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1.0k
views
updating edge visualization rules of an existing graph in RedeR
graph RedeR graph RedeR
updated 8.8 years ago by ▴ 10 • written 8.8 years ago by ▴ 200
0
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1
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1.1k
views
Sciplot: Increasing the width of bargraph and decreasing the sapce b/n groups
graph graph
updated 9.1 years ago by 63k • written 9.1 years ago by ▴ 130
0
votes
5
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3.0k
views
Gviz AnnotationTrack - Consistent y-scales
Coverage Annotation graph Gviz Coverage Annotation graph Gviz
updated 9.1 years ago by ▴ 130 • written 9.1 years ago by ▴ 350
0
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0
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1.0k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
9.1 years ago Kasper Daniel Hansen 6.5k
0
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0
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1.1k
views
Plotting per base coverage from genomecoveragebed utility
graph graph
9.1 years ago gv ▴ 40
0
votes
9
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2.4k
views
Rgraphviz compilation error
graph graph
updated 9.1 years ago by ▴ 70 • written 9.1 years ago by ★ 12k
0
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5
replies
1.3k
views
problem with makeGOGraph function
Yeast graph GOstats Yeast graph GOstats
updated 9.2 years ago by 63k • written 9.2 years ago by ★ 12k
0
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0
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1.6k
views
edgeR: regarding Poisson distribution and goodness of
Normalization graph edgeR Normalization graph edgeR
9.3 years ago Yunshun Chen ▴ 790
0
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0
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1.1k
views
edgeR: regarding Poisson distribution and goodness of fit graph
Normalization graph edgeR Normalization graph edgeR
9.3 years ago Guest User ★ 12k
0
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1
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1.1k
views
how to determine what kind of dispersion to use
graph edgeR graph edgeR
updated 9.3 years ago by 7.8k • written 9.3 years ago by ★ 12k
0
votes
5
replies
4.1k
views
Problem with exporting graph from plotPCA() in a DESeq2 function
graph DESeq2 graph DESeq2
updated 9.3 years ago by 40k • written 9.3 years ago by ★ 12k
0
votes
2
replies
1.9k
views
What RNA-Seq expression estimates to use for plotting to show voom/limma Differential expression
Visualization graph limma Visualization graph limma
updated 9.3 years ago by 47k • written 9.3 years ago by ▴ 30
0
votes
1
reply
910
views
FLowClust/FLowCore
graph flowCore graph flowCore
updated 9.4 years ago by ★ 1.3k • written 9.4 years ago by ★ 12k
0
votes
0
replies
1.3k
views
pathview vectorized output?
Pathways graph pathview Pathways graph pathview
9.4 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.1k
views
Statistics questions regarding the use of Ambion ExFold ERCC standards with Affmetrix ST arrays.
Normalization vsn graph Normalization vsn graph
updated 9.4 years ago by 63k • written 9.4 years ago by ▴ 350
0
votes
4
replies
1.7k
views
RCytoscape: object 'graph' not found error
graph RCytoscape graph RCytoscape
updated 9.4 years ago by ▴ 470 • written 9.4 years ago by ▴ 210
0
votes
1
reply
978
views
bug in graph::addNode() w/ graph::edgeData()
graph graph
updated 9.5 years ago by ★ 3.0k • written 9.5 years ago by ▴ 750
0
votes
2
replies
1.1k
views
bug in graph::addNode() w/ graph::edgeData()
graph graph
updated 9.6 years ago by ▴ 750 • written 9.6 years ago by ★ 3.0k
0
votes
2
replies
2.3k
views
pathview -- ID Problem?
graph pathview graph pathview
updated 9.6 years ago by ▴ 40 • written 9.6 years ago by ★ 1.6k
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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