Showing : kegggraph • reset
1
vote
2
replies
361
views
KEGGgraph result difference
igraph KEGGgraph RCy3 GraphNEL
8 weeks ago • updated 24 days ago Arindam ▴ 80
0
votes
3
replies
550
views
pathview error
KEGGgraph KEGG
updated 5 months ago by ★ 4.1k • written 5 months ago by • 0
1
vote
1
reply
341
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 6 months ago by 67k • written 6 months ago by ▴ 30
4
votes
2
replies
489
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 30
2
votes
2
replies
469
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
0
replies
390
views
Gene names not included on KEGGgraph plots
KEGGgraph
16 months ago hilarius_bookbinder • 0
0
votes
1
reply
676
views
KEGGgraph parseKGML2Graph function
KEGGgraph
updated 23 months ago by 67k • written 24 months ago by • 0
4
votes
2
replies
3.1k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.0 years ago Wuschel ▴ 10
4
votes
6
replies
4.4k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.2 years ago by ★ 4.1k • written 2.4 years ago by ▴ 10
0
votes
3
replies
1.2k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.3 years ago abf ▴ 30
0
votes
1
reply
993
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph pathview
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by • 0
1
vote
2
replies
1.3k
views
cannot find function even though KEGGgraph package supposedly installed
kegggraph biocinstaller
updated 6.3 years ago by ★ 6.6k • written 6.3 years ago by ▴ 10
1
vote
2
replies
2.7k
views
How to get the latest KEGG pathway
KEGG kegg.db kegggraph
6.7 years ago Raymond ▴ 20
1
vote
2
replies
1.3k
views
possible bug in parseKGML?
kegggraph
7.2 years ago Martin Pirkl • 0
2
votes
11
replies
5.1k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.3 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.2k
views
incorrect direction in compound-gene interactions
kegggraph
7.3 years ago AR3513 • 0
0
votes
6
replies
3.4k
views
KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
kegggraph
7.4 years ago AR3513 • 0
0
votes
1
reply
1.1k
views
objNameToList() on some particular list of objects in parent frame
tkWidgets xml kegggraph
updated 7.5 years ago by 67k • written 7.5 years ago by • 0
2
votes
3
replies
3.8k
views
How to convert graphNEL object into Adjacency Matrix?
graph kegggraph xml
updated 7.5 years ago by ★ 3.4k • written 7.5 years ago by • 0
0
votes
5
replies
3.0k
views
retrieve human readable gene names from KEGG identifiers
kegggraph
8.8 years ago Osvaldo ▴ 40
0
votes
7
replies
2.4k
views
Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
graph KEGGgraph graph KEGGgraph
11.1 years ago Zhang, Jitao David ▴ 120
1
vote
5
replies
2.3k
views
About the state of KEGG-related packages
KEGGSOAP KEGGgraph keggorthology clusterProfiler KEGGprofile PathNet KEGGSOAP KEGGgraph
updated 11.3 years ago by ★ 1.6k • written 11.3 years ago by ▴ 660
0
votes
0
replies
1.2k
views
looking for tools to study additive expression effects in gene pathways/networks
Pathways Rgraphviz KEGGgraph Pathways Rgraphviz KEGGgraph
11.5 years ago Christopher T Gregg ▴ 210
0
votes
2
replies
2.0k
views
KEGGgraph problem
KEGGgraph KEGGgraph
updated 11.8 years ago by ▴ 120 • written 11.8 years ago by ★ 13k
0
votes
4
replies
2.1k
views
KEGGgraph
Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph
12.0 years ago Ricardo Silva ▴ 110
0
votes
2
replies
1.4k
views
KEGGgraph
graph KEGGgraph graph KEGGgraph
updated 13.3 years ago by ▴ 340 • written 13.3 years ago by ▴ 380
0
votes
3
replies
2.0k
views
Fwd: KEGGgraph / Rgraphviz dot layout
KEGGgraph KEGGgraph
updated 13.9 years ago by ▴ 340 • written 13.9 years ago by ▴ 40
0
votes
2
replies
1.4k
views
(no subject)
KEGGgraph KEGGgraph
updated 14.0 years ago by ▴ 340 • written 14.0 years ago by ▴ 140
0
votes
0
replies
1.5k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
14.0 years ago Tarca, Adi ▴ 570
0
votes
0
replies
1.2k
views
KEGGgraph and Rgraphviz for win 64
KEGGgraph KEGGgraph
14.0 years ago Yan Jiao ▴ 140
0
votes
1
reply
1.5k
views
About KEGGgraph supplementary information
Rgraphviz KEGGgraph Rgraphviz KEGGgraph
updated 14.0 years ago by ▴ 10 • written 14.0 years ago by ▴ 20
0
votes
0
replies
1.3k
views
error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
14.1 years ago Robert M. Flight ▴ 280
0
votes
3
replies
1.6k
views
error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 14.1 years ago by ▴ 30 • written 14.1 years ago by ▴ 340
0
votes
1
reply
1.3k
views
error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 14.3 years ago by ▴ 340 • written 14.3 years ago by ▴ 280
0
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2
replies
1.8k
views
makeAttr() missing in KEGGgraph
KEGGgraph KEGGgraph
updated 14.5 years ago by 25k • written 14.5 years ago by ▴ 630
0
votes
1
reply
1.9k
views
KEGGgraph: retrieveKGML error (due to wrong ftp path)
KEGGgraph KEGGgraph
updated 14.6 years ago by ▴ 370 • written 14.6 years ago by ▴ 70
0
votes
4
replies
1.8k
views
KEGGgraph fails on a KEGG XML file
KEGGgraph KEGGgraph
updated 14.7 years ago by ▴ 340 • written 14.7 years ago by ▴ 120
0
votes
2
replies
1.7k
views
KEGGgraph: any way to obtain 'outcome' nodes?
Pathways KEGGgraph Pathways KEGGgraph
updated 14.9 years ago by ▴ 270 • written 14.9 years ago by ★ 1.1k
0
votes
1
reply
1.7k
views
KEGGgraph bug
Pathways Organism SIM KEGGgraph Pathways Organism SIM KEGGgraph
updated 14.9 years ago by ★ 7.2k • written 14.9 years ago by ▴ 270
0
votes
1
reply
1.1k
views
KEGGgraph query
Pathways graph KEGGgraph Pathways graph KEGGgraph
updated 15.0 years ago by ▴ 340 • written 15.0 years ago by ▴ 270
0
votes
1
reply
1.6k
views
KEGGgraph bug
Organism KEGGgraph Organism KEGGgraph
updated 15.0 years ago by ▴ 340 • written 15.0 years ago by ▴ 270
0
votes
3
replies
1.8k
views
Problem with KEGGgraph
Organism hgu133plus2 KEGGgraph Organism hgu133plus2 KEGGgraph
updated 15.1 years ago by ▴ 570 • written 15.1 years ago by ▴ 270
0
votes
0
replies
936
views
Important KEGGgraph update (parse issue solved)
KEGGgraph KEGGgraph
15.4 years ago Jitao David Zhang ▴ 340
0
votes
3
replies
2.2k
views
KEGGgraph: gene ids for nodes in a pathway
KEGGgraph KEGGgraph
updated 15.5 years ago by ▴ 340 • written 15.5 years ago by ★ 1.1k
0
votes
4
replies
1.7k
views
KEGGGraph: some complexed proteins are orphans in graphNEL
KEGGgraph KEGGgraph
updated 15.5 years ago by ▴ 340 • written 15.5 years ago by ★ 1.1k
0
votes
1
reply
1.2k
views
KEGGgraph package: KGML files working again
KEGGgraph KEGGgraph
updated 15.6 years ago by ▴ 380 • written 15.6 years ago by ▴ 340
0
votes
7
replies
3.5k
views
Visualise KEGG pathway and highlight genes
Cancer KEGGgraph Cancer KEGGgraph
updated 15.6 years ago by ▴ 140 • written 15.6 years ago by ★ 1.9k
0
votes
2
replies
1.7k
views
KEGGgraph, error
Organism hgu133a KEGGgraph Organism hgu133a KEGGgraph
updated 15.6 years ago by ▴ 20 • written 15.6 years ago by ▴ 380
0
votes
1
reply
1.3k
views
KEGGgraph question
Pathways KEGGgraph Pathways KEGGgraph
15.7 years ago Sim, Fraser ▴ 350
0
votes
0
replies
980
views
KEGGgraph ??
Pathways GO GOstats keggorth KEGGgraph Pathways GO GOstats keggorth KEGGgraph
16.1 years ago Paul Evans ▴ 180
50 results • Page 1 of 1
Recent ...
Replies
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Votes
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
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Popular Question to Guido Hooiveld ★ 4.1k
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Popular Question to shepherl 4.1k
Supporter to Paul Harrison ▴ 100
Popular Question to Mikhail Dozmorov ▴ 30
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