Showing : KEGGgraph • reset
2
votes
11
replies
4.9k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.2 years ago • updated 7.1 years ago Luo Weijun ★ 1.6k
4
votes
6
replies
4.2k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.0 years ago by ★ 4.1k • written 2.2 years ago by ▴ 10
2
votes
3
replies
3.6k
views
How to convert graphNEL object into Adjacency Matrix?
graph kegggraph xml
updated 7.4 years ago by ★ 3.4k • written 7.4 years ago by • 0
0
votes
7
replies
3.5k
views
Visualise KEGG pathway and highlight genes
Cancer KEGGgraph Cancer KEGGgraph
updated 15.4 years ago by ▴ 140 • written 15.4 years ago by ★ 1.9k
0
votes
6
replies
3.3k
views
KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
kegggraph
7.3 years ago • updated 7.2 years ago AR3513 • 0
0
votes
5
replies
3.0k
views
retrieve human readable gene names from KEGG identifiers
kegggraph
8.6 years ago Osvaldo ▴ 40
4
votes
2
replies
2.7k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
23 months ago Wuschel ▴ 10
1
vote
2
replies
2.5k
views
How to get the latest KEGG pathway
KEGG kegg.db kegggraph
6.6 years ago Raymond ▴ 20
0
votes
7
replies
2.3k
views
Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
graph KEGGgraph graph KEGGgraph
10.9 years ago Zhang, Jitao David ▴ 120
1
vote
5
replies
2.2k
views
About the state of KEGG-related packages
KEGGSOAP KEGGgraph keggorthology clusterProfiler KEGGprofile PathNet KEGGSOAP KEGGgraph
updated 11.1 years ago by ★ 1.6k • written 11.1 years ago by ▴ 660
0
votes
3
replies
2.1k
views
KEGGgraph: gene ids for nodes in a pathway
KEGGgraph KEGGgraph
updated 15.4 years ago by ▴ 340 • written 15.4 years ago by ★ 1.1k
0
votes
4
replies
2.0k
views
KEGGgraph
Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph
11.9 years ago Ricardo Silva ▴ 110
0
votes
3
replies
2.0k
views
Fwd: KEGGgraph / Rgraphviz dot layout
KEGGgraph KEGGgraph
updated 13.8 years ago by ▴ 340 • written 13.8 years ago by ▴ 40
0
votes
2
replies
2.0k
views
KEGGgraph problem
KEGGgraph KEGGgraph
updated 11.6 years ago by ▴ 120 • written 11.6 years ago by ★ 13k
0
votes
1
reply
1.9k
views
KEGGgraph: retrieveKGML error (due to wrong ftp path)
KEGGgraph KEGGgraph
updated 14.5 years ago by ▴ 370 • written 14.5 years ago by ▴ 70
0
votes
4
replies
1.8k
views
KEGGgraph fails on a KEGG XML file
KEGGgraph KEGGgraph
updated 14.5 years ago by ▴ 340 • written 14.5 years ago by ▴ 120
0
votes
3
replies
1.7k
views
Problem with KEGGgraph
Organism hgu133plus2 KEGGgraph Organism hgu133plus2 KEGGgraph
updated 14.9 years ago by ▴ 570 • written 14.9 years ago by ▴ 270
0
votes
2
replies
1.7k
views
makeAttr() missing in KEGGgraph
KEGGgraph KEGGgraph
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 630
0
votes
2
replies
1.7k
views
KEGGgraph: any way to obtain 'outcome' nodes?
Pathways KEGGgraph Pathways KEGGgraph
updated 14.8 years ago by ▴ 270 • written 14.8 years ago by ★ 1.1k
0
votes
2
replies
1.6k
views
KEGGgraph, error
Organism hgu133a KEGGgraph Organism hgu133a KEGGgraph
updated 15.4 years ago by ▴ 20 • written 15.4 years ago by ▴ 380
0
votes
1
reply
1.6k
views
KEGGgraph bug
Pathways Organism SIM KEGGgraph Pathways Organism SIM KEGGgraph
updated 14.8 years ago by ★ 7.2k • written 14.8 years ago by ▴ 270
0
votes
4
replies
1.6k
views
KEGGGraph: some complexed proteins are orphans in graphNEL
KEGGgraph KEGGgraph
updated 15.4 years ago by ▴ 340 • written 15.4 years ago by ★ 1.1k
0
votes
3
replies
1.5k
views
error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 14.0 years ago by ▴ 30 • written 14.0 years ago by ▴ 340
0
votes
1
reply
1.5k
views
KEGGgraph bug
Organism KEGGgraph Organism KEGGgraph
updated 14.8 years ago by ▴ 340 • written 14.8 years ago by ▴ 270
0
votes
0
replies
1.4k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
13.8 years ago Tarca, Adi ▴ 570
0
votes
1
reply
1.4k
views
About KEGGgraph supplementary information
Rgraphviz KEGGgraph Rgraphviz KEGGgraph
updated 13.9 years ago by ▴ 10 • written 13.9 years ago by ▴ 20
0
votes
2
replies
1.4k
views
(no subject)
KEGGgraph KEGGgraph
updated 13.8 years ago by ▴ 340 • written 13.8 years ago by ▴ 140
0
votes
2
replies
1.4k
views
KEGGgraph
graph KEGGgraph graph KEGGgraph
updated 13.2 years ago by ▴ 340 • written 13.2 years ago by ▴ 380
1
vote
2
replies
1.3k
views
possible bug in parseKGML?
kegggraph
7.0 years ago Martin Pirkl • 0
0
votes
0
replies
1.3k
views
error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
14.0 years ago Robert M. Flight ▴ 280
0
votes
1
reply
1.2k
views
error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 14.2 years ago by ▴ 340 • written 14.2 years ago by ▴ 280
0
votes
1
reply
1.2k
views
KEGGgraph package: KGML files working again
KEGGgraph KEGGgraph
updated 15.4 years ago by ▴ 380 • written 15.4 years ago by ▴ 340
0
votes
1
reply
1.2k
views
KEGGgraph question
Pathways KEGGgraph Pathways KEGGgraph
15.5 years ago Sim, Fraser ▴ 350
1
vote
2
replies
1.2k
views
cannot find function even though KEGGgraph package supposedly installed
kegggraph biocinstaller
updated 6.1 years ago by ★ 6.5k • written 6.1 years ago by ▴ 10
0
votes
0
replies
1.2k
views
KEGGgraph and Rgraphviz for win 64
KEGGgraph KEGGgraph
13.8 years ago Yan Jiao ▴ 140
0
votes
3
replies
1.2k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.1 years ago abf ▴ 30
0
votes
0
replies
1.1k
views
looking for tools to study additive expression effects in gene pathways/networks
Pathways Rgraphviz KEGGgraph Pathways Rgraphviz KEGGgraph
11.3 years ago Christopher T Gregg ▴ 210
0
votes
2
replies
1.1k
views
incorrect direction in compound-gene interactions
kegggraph
7.2 years ago AR3513 • 0
0
votes
1
reply
1.1k
views
KEGGgraph query
Pathways graph KEGGgraph Pathways graph KEGGgraph
updated 14.8 years ago by ▴ 340 • written 14.8 years ago by ▴ 270
0
votes
1
reply
1.0k
views
objNameToList() on some particular list of objects in parent frame
tkWidgets xml kegggraph
updated 7.4 years ago by 67k • written 7.4 years ago by • 0
0
votes
0
replies
951
views
KEGGgraph ??
Pathways GO GOstats keggorth KEGGgraph Pathways GO GOstats keggorth KEGGgraph
15.9 years ago Paul Evans ▴ 180
0
votes
1
reply
941
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph pathview
updated 2.2 years ago by ★ 4.1k • written 2.3 years ago by • 0
0
votes
0
replies
913
views
Important KEGGgraph update (parse issue solved)
KEGGgraph KEGGgraph
15.3 years ago Jitao David Zhang ▴ 340
0
votes
1
reply
635
views
KEGGgraph parseKGML2Graph function
KEGGgraph
updated 22 months ago by 67k • written 22 months ago by • 0
4
votes
2
replies
417
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 4 months ago by ★ 4.1k • written 4 months ago by ▴ 20
2
votes
2
replies
415
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 6 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
3
replies
403
views
pathview error
KEGGgraph KEGG
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
0
votes
0
replies
364
views
Gene names not included on KEGGgraph plots
KEGGgraph
15 months ago hilarius_bookbinder • 0
1
vote
1
reply
289
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 4 months ago by 67k • written 4 months ago by ▴ 20
0
votes
1
reply
72
views
KEGGgraph result difference
igraph KEGGgraph RCy3 GraphNEL
updated 2 days ago by ▴ 20 • written 2 days ago by ▴ 80
50 results • Page 1 of 1
Recent ...
Replies
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Hello, Thank you. I absolutely respect what you mention about p-values and logFC, I was just going to tackle that soon and thank you for po…
Comment: QSEA:Error in h(simpleError(msg, call)) by kf • 0
genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus by James W. MacDonald 67k
I don't know what you mean by 'a pairwise comparison', but the two analyses are equivalent, except in the second analysis you want to do `t…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k
If you want to comment on an answer, please choose ADD COMMENT rather than ADD ANSWER, since you are not in fact adding an answer. ``` uni…
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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