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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
6.8 years ago • updated 6.7 years ago
Luo Weijun
★ 1.6k
4
votes
6
replies
3.6k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 19 months ago by
Guido Hooiveld
★ 3.9k • written 22 months ago by
rama
▴ 10
2
votes
3
replies
3.4k
views
How to convert graphNEL object into Adjacency Matrix?
graph
kegggraph
xml
updated 7.0 years ago by
Robert Castelo
★ 3.2k • written 7.0 years ago by
urwaCFC
• 0
0
votes
6
replies
3.2k
views
KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
kegggraph
6.9 years ago • updated 6.8 years ago
AR3513
• 0
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
0
votes
5
replies
2.8k
views
retrieve human readable gene names from KEGG identifiers
kegggraph
8.2 years ago
Osvaldo
▴ 40
0
votes
7
replies
2.1k
views
Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
graph
KEGGgraph
graph
KEGGgraph
10.5 years ago
Zhang, Jitao David
▴ 120
1
vote
5
replies
2.0k
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
3
replies
2.0k
views
KEGGgraph: gene ids for nodes in a pathway
KEGGgraph
KEGGgraph
updated 15.0 years ago by
Jitao David Zhang
▴ 340 • written 15.0 years ago by
Tim Smith
★ 1.1k
1
vote
2
replies
1.9k
views
How to get the latest KEGG pathway
KEGG
kegg.db
kegggraph
6.2 years ago
Raymond
▴ 20
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
0
votes
3
replies
1.8k
views
Fwd: KEGGgraph / Rgraphviz dot layout
KEGGgraph
KEGGgraph
updated 13.4 years ago by
Jitao David Zhang
▴ 340 • written 13.4 years ago by
Unger, Kristian
▴ 40
4
votes
2
replies
1.8k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
18 months ago
Wuschel
▴ 10
0
votes
4
replies
1.8k
views
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
Pathways
Organism
graph
PROcess
KEGGgraph
11.5 years ago
Ricardo Silva
▴ 110
0
votes
1
reply
1.8k
views
KEGGgraph: retrieveKGML error (due to wrong ftp path)
KEGGgraph
KEGGgraph
updated 14.1 years ago by
Cristobal Fresno Rodríguez
▴ 370 • written 14.1 years ago by
Ludwig Geistlinger
▴ 70
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
2
replies
1.6k
views
makeAttr() missing in KEGGgraph
KEGGgraph
KEGGgraph
updated 13.9 years ago by
Martin Morgan
25k • written 13.9 years ago by
Groot, Philip de
▴ 630
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
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
1.5k
views
KEGGgraph bug
Pathways
Organism
SIM
KEGGgraph
Pathways
Organism
SIM
KEGGgraph
updated 14.4 years ago by
Marc Carlson
★ 7.2k • written 14.4 years ago by
Fraser Sim
▴ 270
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
4
replies
1.5k
views
KEGGGraph: some complexed proteins are orphans in graphNEL
KEGGgraph
KEGGgraph
updated 15.0 years ago by
Jitao David Zhang
▴ 340 • written 15.0 years ago by
Paul Shannon
★ 1.1k
0
votes
3
replies
1.4k
views
error in plotKEGGGraph
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 13.6 years ago by
Pierre Neuvial
▴ 30 • written 13.6 years ago by
Jitao David Zhang
▴ 340
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
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
13.4 years ago
Tarca, Adi
▴ 570
0
votes
2
replies
1.3k
views
KEGGgraph
graph
KEGGgraph
graph
KEGGgraph
updated 12.8 years ago by
Jitao David Zhang
▴ 340 • written 12.8 years ago by
Jing Huang
▴ 380
0
votes
2
replies
1.3k
views
(no subject)
KEGGgraph
KEGGgraph
updated 13.4 years ago by
Jitao David Zhang
▴ 340 • written 13.4 years ago by
Yan Jiao
▴ 140
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
1
vote
2
replies
1.1k
views
possible bug in parseKGML?
kegggraph
6.6 years ago
Martin Pirkl
• 0
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
1
reply
1.1k
views
KEGGgraph package: KGML files working again
KEGGgraph
KEGGgraph
updated 15.0 years ago by
Markus Schmidberger
▴ 380 • written 15.0 years ago by
Jitao David Zhang
▴ 340
0
votes
0
replies
1.1k
views
KEGGgraph and Rgraphviz for win 64
KEGGgraph
KEGGgraph
13.4 years ago
Yan Jiao
▴ 140
0
votes
1
reply
1.1k
views
KEGGgraph question
Pathways
KEGGgraph
Pathways
KEGGgraph
15.1 years ago
Sim, Fraser
▴ 350
0
votes
1
reply
1.1k
views
error in plotKEGGGraph
Pathways
KEGGgraph
Pathways
KEGGgraph
updated 13.8 years ago by
Jitao David Zhang
▴ 340 • written 13.8 years ago by
Robert M. Flight
▴ 280
1
vote
2
replies
1.1k
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
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
0
votes
1
reply
981
views
KEGGgraph query
Pathways
graph
KEGGgraph
Pathways
graph
KEGGgraph
updated 14.4 years ago by
Jitao David Zhang
▴ 340 • written 14.4 years ago by
anupam sinha
▴ 270
0
votes
2
replies
975
views
incorrect direction in compound-gene interactions
kegggraph
6.8 years ago
AR3513
• 0
0
votes
3
replies
936
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
20 months ago
abf
▴ 30
0
votes
1
reply
893
views
objNameToList() on some particular list of objects in parent frame
tkWidgets
xml
kegggraph
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
urwaCFC
• 0
0
votes
0
replies
855
views
KEGGgraph ??
Pathways
GO
GOstats
keggorth
KEGGgraph
Pathways
GO
GOstats
keggorth
KEGGgraph
15.5 years ago
Paul Evans
▴ 180
0
votes
0
replies
826
views
Important KEGGgraph update (parse issue solved)
KEGGgraph
KEGGgraph
14.9 years ago
Jitao David Zhang
▴ 340
0
votes
1
reply
774
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 22 months ago by
Guido Hooiveld
★ 3.9k • written 22 months ago by
k.jane.olczak
• 0
0
votes
1
reply
501
views
KEGGgraph parseKGML2Graph function
KEGGgraph
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Cathy
• 0
0
votes
0
replies
263
views
Gene names not included on KEGGgraph plots
KEGGgraph
10 months ago
hilarius_bookbinder
• 0
2
votes
2
replies
230
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 8 weeks ago by
Guido Hooiveld
★ 3.9k • written 9 weeks ago by
cinzia.spagnoli
• 0
46 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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