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0
votes
2
replies
3.5k
views
pathview -- ID Problem?
graph
pathview
graph
pathview
updated 12.2 years ago by
fabian
▴ 40 • written 12.2 years ago by
Luo Weijun
★ 1.6k
0
votes
6
replies
4.5k
views
Directed MST (Edmond's Algorithm)
GO
graph
RBGL
GO
graph
RBGL
updated 12.2 years ago by
Steve Lianoglou
★ 13k • written 12.2 years ago by
Forst, Christian
▴ 90
0
votes
1
reply
2.5k
views
deseq2 plotMA
GO
graph
DESeq2
GO
graph
DESeq2
updated 12.2 years ago by
Michael Love
43k • written 12.2 years ago by
Jose M Garcia Manteiga
▴ 310
0
votes
7
replies
2.9k
views
Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
graph
KEGGgraph
graph
KEGGgraph
12.3 years ago • updated 12.2 years ago
Zhang, Jitao David
▴ 120
0
votes
1
reply
2.5k
views
Pathview - Problem with PNG output
Pathways
graph
pathview
Pathways
graph
pathview
updated 12.3 years ago by
Luo Weijun
★ 1.6k • written 12.3 years ago by
Christian De Santis
▴ 150
0
votes
0
replies
1.0k
views
pathview question
graph
graph
12.3 years ago
Luo Weijun
★ 1.6k
0
votes
5
replies
2.2k
views
rsbml package installation error
graph
rsbml
graph
rsbml
updated 12.3 years ago by
Stefan Gries
▴ 50 • written 12.3 years ago by
Michael Lawrence
★ 11k
0
votes
0
replies
2.0k
views
Change enzyme code (EC) into gene symbol
Pathways
graph
pathview
Pathways
graph
pathview
12.4 years ago
Luo Weijun
★ 1.6k
0
votes
4
replies
4.1k
views
Pathview for global and overview maps Re: using pathview about hsa01100
Pathways
graph
PROcess
SIM
gage
pathview
Pathways
graph
PROcess
SIM
gage
pathview
updated 12.4 years ago by
Ed
▴ 230 • written 12.4 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
3.2k
views
Pathview with non-KEGG organisms?
Microbiome
Pathways
GO
Visualization
Organism
graph
gage
pathview
Microbiome
Pathways
GO
12.4 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.4k
views
Error converting SBML to graph Object using R SBML
Network
graph
convert
rsbml
Network
graph
convert
rsbml
12.4 years ago
Michael Lawrence
★ 11k
0
votes
4
replies
1.5k
views
Error converting SBML to graph Object using R SBML
graph
convert
graph
convert
updated 12.5 years ago by
Dan Tenenbaum
★ 8.2k • written 12.5 years ago by
Robin Philip
▴ 20
0
votes
0
replies
3.5k
views
Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation
Pathways
Visualization
graph
PROcess
gage
pathview
Annotation
Pathways
graph
12.5 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.6k
views
Pathview published in Bioinformatics
Visualization
graph
pathview
Visualization
graph
pathview
12.5 years ago
km
▴ 100
0
votes
1
reply
1.9k
views
Rgraphviz multiline edge label
graph
Rgraphviz
graph
Rgraphviz
updated 12.5 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.5 years ago by
Guest User
★ 13k
0
votes
0
replies
2.3k
views
info on pathview
graph
PROcess
pathview
graph
PROcess
pathview
12.5 years ago
Luo Weijun
★ 1.6k
0
votes
3
replies
2.1k
views
rsbml package installation error
graph
rsbml
graph
rsbml
updated 12.6 years ago by
Michael Lawrence
★ 11k • written 12.6 years ago by
Stefan Gries
▴ 50
0
votes
0
replies
1.5k
views
pathview
Pathways
graph
pathview
Pathways
graph
pathview
12.6 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.2k
views
DEXSeq: PlotMA issues
graph
DESeq
DEXSeq
graph
DESeq
DEXSeq
12.6 years ago
Alejandro Reyes
★ 1.9k
0
votes
1
reply
1.2k
views
Doubt RCytoscape
graph
graph
updated 12.7 years ago by
Paul Shannon
▴ 750 • written 12.7 years ago by
Ricardo Silva
▴ 110
1
vote
1
reply
2.2k
views
topGO Fisher test error
GO
graph
GO
graph
updated 12.8 years ago by
Adrian Alexa
▴ 400 • written 12.8 years ago by
Guest User
★ 13k
0
votes
0
replies
1.1k
views
two color arrays, LIMMA and GOstats analysis
Clustering
graph
Clustering
graph
12.8 years ago
Andreas Heider
▴ 340
0
votes
1
reply
1.4k
views
5000 nodes RCytoscape
Network
graph
Network
graph
12.8 years ago
Paul Shannon
▴ 750
0
votes
3
replies
1.4k
views
bug in graph::edgeData()
graph
graph
updated 12.9 years ago by
Paul Shannon
▴ 750 • written 12.9 years ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
1.3k
views
graph::subGraph() problem with node attributes
graph
graph
updated 12.9 years ago by
Valerie Obenchain
★ 6.8k • written 12.9 years ago by
Robert Castelo
★ 3.4k
0
votes
2
replies
2.0k
views
GSEABase error parsing msigdb_v3.1.xml
GO
Infrastructure
hgu95av2
Biobase
annotate
graph
Category
AnnotationDbi
BiocGenerics
GO
updated 12.9 years ago by
Martin Morgan
25k • written 12.9 years ago by
Lina Hultin-Rosenberg
▴ 80
1
vote
0
replies
1.2k
views
GO graphs made with topGO are unreadable
GO
graph
topGO
GO
graph
topGO
13.0 years ago
Guest User
★ 13k
0
votes
2
replies
4.5k
views
Offline Installation of Packages and Dependencies
graph
graph
updated 13.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 13.1 years ago by
Nathan Bihlmeyer
▴ 20
0
votes
2
replies
2.1k
views
nodeRenderInfo fill property not working with graph/Rgraphviz
graph
Rgraphviz
graph
Rgraphviz
updated 13.2 years ago by
Kasper Daniel Hansen
★ 6.5k • written 13.2 years ago by
Cristobal Fresno Rodríguez
▴ 370
0
votes
4
replies
3.1k
views
goseq analysis
GO
graph
edgeR
goseq
GO
graph
edgeR
goseq
updated 13.2 years ago by
Alicia Oshlack
▴ 100 • written 13.2 years ago by
Dave Tang
▴ 210
0
votes
4
replies
2.4k
views
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
13.2 years ago
Ricardo Silva
▴ 110
0
votes
1
reply
1.5k
views
EdgeR GOF non-linear
Sequencing
graph
edgeR
Sequencing
graph
edgeR
updated 13.2 years ago by
Gordon Smyth
53k • written 13.2 years ago by
Thomas Frederick Willems
▴ 20
0
votes
0
replies
851
views
limma and legacy data
Microarray
GO
graph
limma
Microarray
GO
graph
limma
13.2 years ago
Simon Melov
▴ 340
0
votes
1
reply
1.1k
views
Analysis of chIP-chip
graph
graph
updated 13.2 years ago by
Joern Toedling
▴ 50 • written 13.2 years ago by
Guest User
★ 13k
0
votes
0
replies
1.2k
views
Rgraphviz plot with edge weights
graph
graph
13.2 years ago
Sam Steingold
▴ 30
0
votes
1
reply
899
views
Question on survival
graph
graph
updated 13.2 years ago by
James W. MacDonald
68k • written 13.3 years ago by
lau pel
▴ 30
1
vote
2
replies
1.4k
views
DEXSeq: Difference in splicing
graph
DEXSeq
graph
DEXSeq
updated 13.3 years ago by
Alejandro Reyes
★ 1.9k • written 13.3 years ago by
Guest User
★ 13k
0
votes
7
replies
2.2k
views
GeneAnswer package Query
Network
graph
Network
graph
updated 13.4 years ago by
Gilbert Feng
▴ 300 • written 13.4 years ago by
Reema Singh
▴ 570
0
votes
0
replies
1.0k
views
Can I adjust family relationship in Limma?
Microarray
graph
limma
Microarray
graph
limma
13.4 years ago
Gordon Smyth
53k
0
votes
0
replies
1.1k
views
BioPAX parsing
Pathways
Visualization
Network
graph
Pathways
Visualization
Network
graph
13.5 years ago
Oliver Ruebenacker
▴ 110
0
votes
0
replies
1.8k
views
Overlapping ROC plots
Classification
ROC
graph
Classification
ROC
graph
13.5 years ago
Yadav Sapkota
▴ 130
0
votes
1
reply
2.3k
views
estimateDispersions in DESeq
Genetics
graph
DESeq
Genetics
graph
DESeq
updated 13.6 years ago by
Wolfgang Huber
★ 13k • written 13.6 years ago by
Flavia Nunes
▴ 10
0
votes
0
replies
1.3k
views
changes to RBGL
graph
RBGL
graph
RBGL
13.6 years ago
Vincent J. Carey, Jr.
6.7k
0
votes
8
replies
2.9k
views
BioPAX parsing
graph
graph
updated 13.6 years ago by
Oliver Ruebenacker
▴ 110 • written 13.6 years ago by
Martin Preusse
▴ 100
0
votes
1
reply
3.9k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 3.0 years ago by
Gordon Smyth
53k • written 13.6 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
4
replies
4.0k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
GO
graph
Rsubread
Normalization
GO
graph
Rsubread
updated 13.6 years ago by
Gordon Smyth
53k • written 13.6 years ago by
Tim Triche
★ 4.2k
0
votes
0
replies
1.1k
views
normalize GFP expression by cell size and graph with densityplot
graph
graph
13.7 years ago
Chandra Jack
▴ 90
0
votes
0
replies
883
views
edge-less pathways in graphite
Pathways
graph
Pathways
graph
13.7 years ago
Paul Shannon
▴ 750
0
votes
1
reply
2.0k
views
deprecated head file for RBGL and compilation failure
graph
RBGL
PROcess
graph
RBGL
PROcess
updated 13.7 years ago by
Vincent J. Carey, Jr.
6.7k • written 13.7 years ago by
Guest User
★ 13k
0
votes
0
replies
1.3k
views
Rgraphviz and node label placement
GO
graph
GO
graph
13.8 years ago
Paul Murrell
▴ 60
360 results • Page
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Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Votes
A: What is logFC and "B" in methylation analysis ??
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
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