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KEGGgraph
•
reset
2
votes
11
replies
3.5k
views
Recent build and parsing error in pathview
pathview
KEGGgraph
gage
pathway
pathway analysis
5.9 years ago • updated 5.8 years ago
Luo Weijun
★ 1.6k
0
votes
6
replies
2.9k
views
KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
kegggraph
6.0 years ago • updated 5.9 years ago
AR3513
• 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
Robert Castelo
★ 3.0k • written 6.1 years ago by
urwaCFC
• 0
0
votes
5
replies
2.5k
views
retrieve human readable gene names from KEGG identifiers
kegggraph
7.3 years ago
Osvaldo
▴ 40
0
votes
7
replies
2.5k
views
Visualise KEGG pathway and highlight genes
Cancer
KEGGgraph
Cancer
KEGGgraph
updated 14.1 years ago by
Paolo Sonego
▴ 140 • written 14.1 years ago by
Daniel Brewer
★ 1.9k
4
votes
6
replies
1.8k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 9 months ago by
Guido Hooiveld
★ 3.6k • written 11 months ago by
rama
▴ 10
0
votes
7
replies
1.6k
views
Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
graph
KEGGgraph
graph
KEGGgraph
9.6 years ago
Zhang, Jitao David
▴ 120
0
votes
2
replies
1.6k
views
KEGGgraph problem
KEGGgraph
KEGGgraph
updated 10.3 years ago by
Zhang, Jitao David
▴ 120 • written 10.3 years ago by
Guest User
★ 12k
0
votes
3
replies
1.6k
views
KEGGgraph: gene ids for nodes in a pathway
KEGGgraph
KEGGgraph
updated 14.1 years ago by
Jitao David Zhang
▴ 340 • written 14.1 years ago by
Tim Smith
★ 1.1k
0
votes
1
reply
1.5k
views
KEGGgraph: retrieveKGML error (due to wrong ftp path)
KEGGgraph
KEGGgraph
updated 13.2 years ago by
Cristobal Fresno Rodríguez
▴ 370 • written 13.2 years ago by
Ludwig Geistlinger
▴ 50
1
vote
5
replies
1.5k
views
About the state of KEGG-related packages
KEGGSOAP
KEGGgraph
keggorthology
clusterProfiler
KEGGprofile
PathNet
KEGGSOAP
KEGGgraph
updated 9.8 years ago by
Luo Weijun
★ 1.6k • written 9.8 years ago by
enricoferrero
▴ 660
0
votes
3
replies
1.5k
views
Fwd: KEGGgraph / Rgraphviz dot layout
KEGGgraph
KEGGgraph
updated 12.5 years ago by
Jitao David Zhang
▴ 340 • written 12.5 years ago by
Unger, Kristian
▴ 40
0
votes
4
replies
1.4k
views
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
10.6 years ago
Ricardo Silva
▴ 110
0
votes
2
replies
1.3k
views
makeAttr() missing in KEGGgraph
KEGGgraph
KEGGgraph
updated 13.0 years ago by
Martin Morgan
25k • written 13.0 years ago by
Groot, Philip de
▴ 630
0
votes
3
replies
1.3k
views
Problem with KEGGgraph
Organism
hgu133plus2
KEGGgraph
Organism
hgu133plus2
KEGGgraph
updated 13.6 years ago by
Tony Chiang
▴ 570 • written 13.6 years ago by
Fraser Sim
▴ 270
0
votes
4
replies
1.3k
views
KEGGgraph fails on a KEGG XML file
KEGGgraph
KEGGgraph
updated 13.2 years ago by
Jitao David Zhang
▴ 340 • written 13.2 years ago by
Rajarshi Guha
▴ 120
0
votes
1
reply
1.2k
views
KEGGgraph bug
Pathways
Organism
SIM
KEGGgraph
Pathways
Organism
SIM
KEGGgraph
updated 13.5 years ago by
Marc Carlson
★ 7.2k • written 13.5 years ago by
Fraser Sim
▴ 270
0
votes
2
replies
1.2k
views
KEGGgraph, error
Organism
hgu133a
KEGGgraph
Organism
hgu133a
KEGGgraph
updated 14.1 years ago by
Jitao Zhang
▴ 20 • written 14.1 years ago by
Markus Schmidberger
▴ 380
0
votes
2
replies
1.2k
views
KEGGgraph: any way to obtain 'outcome' nodes?
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 13.5 years ago by
Fraser Sim
▴ 270 • written 13.5 years ago by
Paul Shannon
★ 1.1k
0
votes
3
replies
1.1k
views
error in plotKEGGGraph
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 12.7 years ago by
Pierre Neuvial
▴ 30 • written 12.7 years ago by
Jitao David Zhang
▴ 340
1
vote
2
replies
1.1k
views
How to get the latest KEGG pathway
KEGG
kegg.db
kegggraph
5.3 years ago
Raymond
▴ 20
0
votes
1
reply
1.1k
views
KEGGgraph bug
Organism
KEGGgraph
Organism
KEGGgraph
updated 13.5 years ago by
Jitao David Zhang
▴ 340 • written 13.5 years ago by
Fraser Sim
▴ 270
0
votes
0
replies
1.1k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism
KEGGgraph
SPIA
Organism
KEGGgraph
SPIA
12.5 years ago
Tarca, Adi
▴ 570
0
votes
4
replies
1.0k
views
KEGGGraph: some complexed proteins are orphans in graphNEL
KEGGgraph
KEGGgraph
updated 14.1 years ago by
Jitao David Zhang
▴ 340 • written 14.1 years ago by
Paul Shannon
★ 1.1k
0
votes
2
replies
1.0k
views
KEGGgraph
graph
KEGGgraph
graph
KEGGgraph
updated 11.9 years ago by
Jitao David Zhang
▴ 340 • written 11.9 years ago by
Jing Huang
▴ 380
0
votes
2
replies
980
views
(no subject)
KEGGgraph
KEGGgraph
updated 12.5 years ago by
Jitao David Zhang
▴ 340 • written 12.5 years ago by
Yan Jiao
▴ 140
0
votes
0
replies
964
views
KEGGgraph and Rgraphviz for win 64
KEGGgraph
KEGGgraph
12.5 years ago
Yan Jiao
▴ 140
0
votes
1
reply
959
views
About KEGGgraph supplementary information
Rgraphviz
KEGGgraph
Rgraphviz
KEGGgraph
updated 12.6 years ago by
Uzun, Alper
▴ 10 • written 12.6 years ago by
Jitao Zhang
▴ 20
0
votes
0
replies
939
views
error in plotKEGGGraph
Pathways
GLAD
KEGGgraph
Pathways
GLAD
KEGGgraph
12.7 years ago
Robert M. Flight
▴ 280
0
votes
1
reply
890
views
KEGGgraph package: KGML files working again
KEGGgraph
KEGGgraph
updated 14.1 years ago by
Markus Schmidberger
▴ 380 • written 14.1 years ago by
Jitao David Zhang
▴ 340
1
vote
2
replies
865
views
possible bug in parseKGML?
kegggraph
5.7 years ago
Martin Pirkl
• 0
0
votes
1
reply
844
views
error in plotKEGGGraph
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 12.9 years ago by
Jitao David Zhang
▴ 340 • written 12.9 years ago by
Robert M. Flight
▴ 280
0
votes
0
replies
838
views
looking for tools to study additive expression effects in gene pathways/networks
Pathways
Rgraphviz
KEGGgraph
Pathways
Rgraphviz
KEGGgraph
10.0 years ago
Christopher T Gregg
▴ 210
0
votes
1
reply
790
views
KEGGgraph question
Pathways
KEGGgraph
Pathways
KEGGgraph
14.3 years ago • updated 14.2 years ago
Sim, Fraser
▴ 350
1
vote
2
replies
784
views
cannot find function even though KEGGgraph package supposedly installed
kegggraph
biocinstaller
updated 4.9 years ago by
Mike Smith
★ 6.0k • written 4.9 years ago by
kathleenfix
▴ 10
0
votes
1
reply
769
views
KEGGgraph query
Pathways
graph
KEGGgraph
Pathways
graph
KEGGgraph
updated 13.5 years ago by
Jitao David Zhang
▴ 340 • written 13.5 years ago by
anupam sinha
▴ 270
0
votes
2
replies
747
views
incorrect direction in compound-gene interactions
kegggraph
5.9 years ago
AR3513
• 0
0
votes
0
replies
694
views
KEGGgraph ??
Pathways
GO
GOstats
keggorth
KEGGgraph
Pathways
GO
GOstats
keggorth
KEGGgraph
14.7 years ago
Paul Evans
▴ 180
0
votes
1
reply
684
views
objNameToList() on some particular list of objects in parent frame
tkWidgets
xml
kegggraph
updated 6.1 years ago by
James W. MacDonald
63k • written 6.1 years ago by
urwaCFC
• 0
0
votes
0
replies
647
views
Important KEGGgraph update (parse issue solved)
KEGGgraph
KEGGgraph
14.0 years ago
Jitao David Zhang
▴ 340
0
votes
3
replies
497
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
9 months ago
abf
▴ 30
4
votes
2
replies
467
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
7 months ago
Wuschel
▴ 10
0
votes
1
reply
372
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 11 months ago by
Guido Hooiveld
★ 3.6k • written 11 months ago by
k.jane.olczak
• 0
0
votes
1
reply
174
views
KEGGgraph parseKGML2Graph function
KEGGgraph
updated 6 months ago by
James W. MacDonald
63k • written 6 months ago by
Cathy
• 0
44 results • Page
1 of 1
Recent ...
Replies
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis
by
mohammedtoufiq91
▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Comment: Question on constructing design matrix and defining contrasts for analysis
by
Gordon Smyth
47k
PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would to the job.
Comment: Question on constructing design matrix and defining contrasts for analysis
by
Gordon Smyth
47k
> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl
by
ansleyharralson
• 0
Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.
Votes
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
Comment: Question on constructing design matrix and defining contrasts for analysis
Comment: Question on constructing design matrix and defining contrasts for analysis
Answer: Question on constructing design matrix and defining contrasts for analysis
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