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kegggraph
•
reset
2
votes
11
replies
4.4k
views
Recent build and parsing error in pathview
pathview
KEGGgraph
gage
pathway
pathway analysis
6.7 years ago
Luo Weijun
★ 1.6k
0
votes
7
replies
2.0k
views
Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
graph
KEGGgraph
graph
KEGGgraph
10.5 years ago
Zhang, Jitao David
▴ 120
0
votes
7
replies
3.1k
views
Visualise KEGG pathway and highlight genes
Cancer
KEGGgraph
Cancer
KEGGgraph
updated 15.0 years ago by
Paolo Sonego
▴ 140 • written 15.0 years ago by
Daniel Brewer
★ 1.9k
4
votes
6
replies
3.5k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 19 months ago by
Guido Hooiveld
★ 3.9k • written 21 months ago by
rama
▴ 10
0
votes
6
replies
3.2k
views
KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
kegggraph
6.8 years ago
AR3513
• 0
0
votes
5
replies
2.8k
views
retrieve human readable gene names from KEGG identifiers
kegggraph
8.1 years ago
Osvaldo
▴ 40
1
vote
5
replies
1.9k
views
About the state of KEGG-related packages
KEGGSOAP
KEGGgraph
keggorthology
clusterProfiler
KEGGprofile
PathNet
KEGGSOAP
KEGGgraph
updated 10.7 years ago by
Luo Weijun
★ 1.6k • written 10.7 years ago by
enricoferrero
▴ 660
0
votes
4
replies
1.4k
views
KEGGGraph: some complexed proteins are orphans in graphNEL
KEGGgraph
KEGGgraph
updated 14.9 years ago by
Jitao David Zhang
▴ 340 • written 14.9 years ago by
Paul Shannon
★ 1.1k
0
votes
4
replies
1.6k
views
KEGGgraph fails on a KEGG XML file
KEGGgraph
KEGGgraph
updated 14.1 years ago by
Jitao David Zhang
▴ 340 • written 14.1 years ago by
Rajarshi Guha
▴ 120
0
votes
4
replies
1.8k
views
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
11.4 years ago
Ricardo Silva
▴ 110
0
votes
3
replies
1.8k
views
Fwd: KEGGgraph / Rgraphviz dot layout
KEGGgraph
KEGGgraph
updated 13.3 years ago by
Jitao David Zhang
▴ 340 • written 13.3 years ago by
Unger, Kristian
▴ 40
0
votes
3
replies
1.9k
views
KEGGgraph: gene ids for nodes in a pathway
KEGGgraph
KEGGgraph
updated 14.9 years ago by
Jitao David Zhang
▴ 340 • written 14.9 years ago by
Tim Smith
★ 1.1k
0
votes
3
replies
1.6k
views
Problem with KEGGgraph
Organism
hgu133plus2
KEGGgraph
Organism
hgu133plus2
KEGGgraph
updated 14.5 years ago by
Tony Chiang
▴ 570 • written 14.5 years ago by
Fraser Sim
▴ 270
0
votes
3
replies
1.4k
views
error in plotKEGGGraph
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 13.5 years ago by
Pierre Neuvial
▴ 30 • written 13.5 years ago by
Jitao David Zhang
▴ 340
2
votes
3
replies
3.3k
views
How to convert graphNEL object into Adjacency Matrix?
graph
kegggraph
xml
updated 6.9 years ago by
Robert Castelo
★ 3.1k • written 6.9 years ago by
urwaCFC
• 0
0
votes
3
replies
907
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
20 months ago
abf
▴ 30
0
votes
2
replies
1.6k
views
makeAttr() missing in KEGGgraph
KEGGgraph
KEGGgraph
updated 13.8 years ago by
Martin Morgan
25k • written 13.8 years ago by
Groot, Philip de
▴ 630
0
votes
2
replies
1.3k
views
(no subject)
KEGGgraph
KEGGgraph
updated 13.3 years ago by
Jitao David Zhang
▴ 340 • written 13.3 years ago by
Yan Jiao
▴ 140
0
votes
2
replies
1.3k
views
KEGGgraph
graph
KEGGgraph
graph
KEGGgraph
updated 12.7 years ago by
Jitao David Zhang
▴ 340 • written 12.7 years ago by
Jing Huang
▴ 380
0
votes
2
replies
1.8k
views
KEGGgraph problem
KEGGgraph
KEGGgraph
updated 11.2 years ago by
Zhang, Jitao David
▴ 120 • written 11.2 years ago by
Guest User
★ 13k
4
votes
2
replies
1.7k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
17 months ago
Wuschel
▴ 10
0
votes
2
replies
1.5k
views
KEGGgraph, error
Organism
hgu133a
KEGGgraph
Organism
hgu133a
KEGGgraph
updated 15.0 years ago by
Jitao Zhang
▴ 20 • written 15.0 years ago by
Markus Schmidberger
▴ 380
0
votes
2
replies
949
views
incorrect direction in compound-gene interactions
kegggraph
6.7 years ago
AR3513
• 0
1
vote
2
replies
1.1k
views
possible bug in parseKGML?
kegggraph
6.6 years ago
Martin Pirkl
• 0
1
vote
2
replies
1.9k
views
How to get the latest KEGG pathway
KEGG
kegg.db
kegggraph
6.1 years ago
Raymond
▴ 20
1
vote
2
replies
1.0k
views
cannot find function even though KEGGgraph package supposedly installed
kegggraph
biocinstaller
updated 5.7 years ago by
Mike Smith
★ 6.5k • written 5.7 years ago by
kathleenfix
▴ 10
2
votes
2
replies
204
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
cinzia.spagnoli
• 0
0
votes
2
replies
1.5k
views
KEGGgraph: any way to obtain 'outcome' nodes?
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 14.3 years ago by
Fraser Sim
▴ 270 • written 14.3 years ago by
Paul Shannon
★ 1.1k
0
votes
1
reply
1.4k
views
KEGGgraph bug
Organism
KEGGgraph
Organism
KEGGgraph
updated 14.4 years ago by
Jitao David Zhang
▴ 340 • written 14.4 years ago by
Fraser Sim
▴ 270
0
votes
1
reply
1.8k
views
KEGGgraph: retrieveKGML error (due to wrong ftp path)
KEGGgraph
KEGGgraph
updated 14.0 years ago by
Cristobal Fresno Rodríguez
▴ 370 • written 14.0 years ago by
Ludwig Geistlinger
▴ 70
0
votes
1
reply
1.1k
views
error in plotKEGGGraph
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 13.7 years ago by
Jitao David Zhang
▴ 340 • written 13.7 years ago by
Robert M. Flight
▴ 280
0
votes
1
reply
750
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 21 months ago by
Guido Hooiveld
★ 3.9k • written 21 months ago by
k.jane.olczak
• 0
0
votes
1
reply
1.2k
views
About KEGGgraph supplementary information
Rgraphviz
KEGGgraph
Rgraphviz
KEGGgraph
updated 13.4 years ago by
Uzun, Alper
▴ 10 • written 13.4 years ago by
Jitao Zhang
▴ 20
0
votes
1
reply
1.1k
views
KEGGgraph question
Pathways
KEGGgraph
Pathways
KEGGgraph
15.1 years ago • updated 15.0 years ago
Sim, Fraser
▴ 350
0
votes
1
reply
477
views
KEGGgraph parseKGML2Graph function
KEGGgraph
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
Cathy
• 0
0
votes
1
reply
967
views
KEGGgraph query
Pathways
graph
KEGGgraph
Pathways
graph
KEGGgraph
updated 14.3 years ago by
Jitao David Zhang
▴ 340 • written 14.3 years ago by
anupam sinha
▴ 270
0
votes
1
reply
1.1k
views
KEGGgraph package: KGML files working again
KEGGgraph
KEGGgraph
updated 14.9 years ago by
Markus Schmidberger
▴ 380 • written 14.9 years ago by
Jitao David Zhang
▴ 340
0
votes
1
reply
1.5k
views
KEGGgraph bug
Pathways
Organism
SIM
KEGGgraph
Pathways
Organism
SIM
KEGGgraph
updated 14.3 years ago by
Marc Carlson
★ 7.2k • written 14.3 years ago by
Fraser Sim
▴ 270
0
votes
1
reply
883
views
objNameToList() on some particular list of objects in parent frame
tkWidgets
xml
kegggraph
updated 6.9 years ago by
James W. MacDonald
65k • written 6.9 years ago by
urwaCFC
• 0
0
votes
0
replies
814
views
Important KEGGgraph update (parse issue solved)
KEGGgraph
KEGGgraph
14.8 years ago
Jitao David Zhang
▴ 340
0
votes
0
replies
1.1k
views
error in plotKEGGGraph
Pathways
GLAD
KEGGgraph
Pathways
GLAD
KEGGgraph
13.5 years ago
Robert M. Flight
▴ 280
0
votes
0
replies
250
views
Gene names not included on KEGGgraph plots
KEGGgraph
9 months ago
hilarius_bookbinder
• 0
0
votes
0
replies
1.1k
views
KEGGgraph and Rgraphviz for win 64
KEGGgraph
KEGGgraph
13.3 years ago
Yan Jiao
▴ 140
0
votes
0
replies
1.3k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism
KEGGgraph
SPIA
Organism
KEGGgraph
SPIA
13.3 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
843
views
KEGGgraph ??
Pathways
GO
GOstats
keggorth
KEGGgraph
Pathways
GO
GOstats
keggorth
KEGGgraph
15.5 years ago
Paul Evans
▴ 180
0
votes
0
replies
1.0k
views
looking for tools to study additive expression effects in gene pathways/networks
Pathways
Rgraphviz
KEGGgraph
Pathways
Rgraphviz
KEGGgraph
10.9 years ago
Christopher T Gregg
▴ 210
46 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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