Showing : kegggraph • reset
1
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2
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563
views
KEGGgraph result difference
igraph KEGGgraph RCy3 GraphNEL
7 months ago • updated 6 months ago Arindam ▴ 80
0
votes
3
replies
951
views
pathview error
KEGGgraph KEGG
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
1
vote
1
reply
495
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 12 months ago by 68k • written 12 months ago by ▴ 30
4
votes
2
replies
690
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 30
2
votes
2
replies
597
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
0
replies
449
views
Gene names not included on KEGGgraph plots
KEGGgraph
22 months ago hilarius_bookbinder • 0
0
votes
1
reply
803
views
KEGGgraph parseKGML2Graph function
KEGGgraph
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
4
votes
2
replies
4.3k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.5 years ago Wuschel ▴ 10
4
votes
6
replies
5.2k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.7 years ago by ★ 4.1k • written 2.8 years ago by ▴ 10
0
votes
3
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1.4k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.7 years ago abf ▴ 30
0
votes
1
reply
1.1k
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph pathview
updated 2.8 years ago by ★ 4.1k • written 2.9 years ago by • 0
1
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2
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1.4k
views
cannot find function even though KEGGgraph package supposedly installed
kegggraph biocinstaller
updated 6.8 years ago by ★ 6.6k • written 6.8 years ago by ▴ 10
1
vote
2
replies
3.5k
views
How to get the latest KEGG pathway
KEGG kegg.db kegggraph
7.2 years ago Raymond ▴ 20
1
vote
2
replies
1.5k
views
possible bug in parseKGML?
kegggraph
7.6 years ago Martin Pirkl • 0
2
votes
11
replies
5.5k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.8 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.3k
views
incorrect direction in compound-gene interactions
kegggraph
7.8 years ago AR3513 • 0
0
votes
6
replies
3.6k
views
KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
kegggraph
7.9 years ago • updated 7.8 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 8.0 years ago by 68k • written 8.0 years ago by • 0
2
votes
3
replies
4.1k
views
How to convert graphNEL object into Adjacency Matrix?
graph kegggraph xml
updated 8.0 years ago by ★ 3.4k • written 8.0 years ago by • 0
0
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5
replies
3.2k
views
retrieve human readable gene names from KEGG identifiers
kegggraph
9.2 years ago Osvaldo ▴ 40
0
votes
7
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2.6k
views
Using KeggGraph's KEGGpathway2reactionGraph and mergeKEGGgraphs functions
graph KEGGgraph graph KEGGgraph
11.6 years ago • updated 11.5 years ago Zhang, Jitao David ▴ 120
1
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5
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2.5k
views
About the state of KEGG-related packages
KEGGSOAP KEGGgraph keggorthology clusterProfiler KEGGprofile PathNet KEGGSOAP KEGGgraph
updated 11.8 years ago by ★ 1.6k • written 11.8 years ago by ▴ 680
0
votes
0
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1.2k
views
looking for tools to study additive expression effects in gene pathways/networks
Pathways Rgraphviz KEGGgraph Pathways Rgraphviz KEGGgraph
12.0 years ago Christopher T Gregg ▴ 210
0
votes
2
replies
2.1k
views
KEGGgraph problem
KEGGgraph KEGGgraph
updated 12.2 years ago by ▴ 120 • written 12.2 years ago by ★ 13k
0
votes
4
replies
2.2k
views
KEGGgraph
Pathways Organism graph PROcess KEGGgraph Pathways Organism graph PROcess KEGGgraph
12.5 years ago Ricardo Silva ▴ 110
0
votes
2
replies
1.5k
views
KEGGgraph
graph KEGGgraph graph KEGGgraph
updated 13.8 years ago by ▴ 340 • written 13.8 years ago by ▴ 380
0
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3
replies
2.2k
views
Fwd: KEGGgraph / Rgraphviz dot layout
KEGGgraph KEGGgraph
updated 14.4 years ago by ▴ 340 • written 14.4 years ago by ▴ 40
0
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2
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1.5k
views
(no subject)
KEGGgraph KEGGgraph
updated 14.4 years ago by ▴ 340 • written 14.4 years ago by ▴ 140
0
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0
replies
1.6k
views
Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
Organism KEGGgraph SPIA Organism KEGGgraph SPIA
14.4 years ago Tarca, Adi ▴ 570
0
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0
replies
1.3k
views
KEGGgraph and Rgraphviz for win 64
KEGGgraph KEGGgraph
14.4 years ago Yan Jiao ▴ 140
0
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1
reply
1.6k
views
About KEGGgraph supplementary information
Rgraphviz KEGGgraph Rgraphviz KEGGgraph
updated 14.5 years ago by ▴ 10 • written 14.5 years ago by ▴ 20
0
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0
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1.4k
views
error in plotKEGGGraph
Pathways GLAD KEGGgraph Pathways GLAD KEGGgraph
14.6 years ago Robert M. Flight ▴ 280
0
votes
3
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1.7k
views
error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 14.6 years ago by ▴ 30 • written 14.6 years ago by ▴ 340
0
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1
reply
1.4k
views
error in plotKEGGGraph
Pathways KEGGgraph Pathways KEGGgraph
updated 14.8 years ago by ▴ 340 • written 14.8 years ago by ▴ 280
0
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2
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1.9k
views
makeAttr() missing in KEGGgraph
KEGGgraph KEGGgraph
updated 14.9 years ago by 25k • written 14.9 years ago by ▴ 630
0
votes
1
reply
2.0k
views
KEGGgraph: retrieveKGML error (due to wrong ftp path)
KEGGgraph KEGGgraph
updated 15.1 years ago by ▴ 370 • written 15.1 years ago by ▴ 70
0
votes
4
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2.0k
views
KEGGgraph fails on a KEGG XML file
KEGGgraph KEGGgraph
updated 15.1 years ago by ▴ 340 • written 15.2 years ago by ▴ 120
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2
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1.9k
views
KEGGgraph: any way to obtain 'outcome' nodes?
Pathways KEGGgraph Pathways KEGGgraph
updated 15.4 years ago by ▴ 270 • written 15.4 years ago by ★ 1.1k
0
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1
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1.7k
views
KEGGgraph bug
Pathways Organism SIM KEGGgraph Pathways Organism SIM KEGGgraph
updated 15.4 years ago by ★ 7.2k • written 15.4 years ago by ▴ 270
0
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1
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1.2k
views
KEGGgraph query
Pathways graph KEGGgraph Pathways graph KEGGgraph
updated 15.4 years ago by ▴ 340 • written 15.4 years ago by ▴ 270
0
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1
reply
1.7k
views
KEGGgraph bug
Organism KEGGgraph Organism KEGGgraph
updated 15.4 years ago by ▴ 340 • written 15.4 years ago by ▴ 270
0
votes
3
replies
1.9k
views
Problem with KEGGgraph
Organism hgu133plus2 KEGGgraph Organism hgu133plus2 KEGGgraph
updated 15.5 years ago by ▴ 570 • written 15.5 years ago by ▴ 270
0
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0
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1.0k
views
Important KEGGgraph update (parse issue solved)
KEGGgraph KEGGgraph
15.9 years ago Jitao David Zhang ▴ 340
0
votes
3
replies
2.3k
views
KEGGgraph: gene ids for nodes in a pathway
KEGGgraph KEGGgraph
updated 16.0 years ago by ▴ 340 • written 16.0 years ago by ★ 1.1k
0
votes
4
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1.8k
views
KEGGGraph: some complexed proteins are orphans in graphNEL
KEGGgraph KEGGgraph
updated 16.0 years ago by ▴ 340 • written 16.0 years ago by ★ 1.1k
0
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1
reply
1.3k
views
KEGGgraph package: KGML files working again
KEGGgraph KEGGgraph
updated 16.0 years ago by ▴ 380 • written 16.0 years ago by ▴ 340
0
votes
7
replies
3.9k
views
Visualise KEGG pathway and highlight genes
Cancer KEGGgraph Cancer KEGGgraph
updated 16.0 years ago by ▴ 140 • written 16.0 years ago by ★ 1.9k
0
votes
2
replies
1.8k
views
KEGGgraph, error
Organism hgu133a KEGGgraph Organism hgu133a KEGGgraph
updated 16.0 years ago by ▴ 20 • written 16.0 years ago by ▴ 380
0
votes
1
reply
1.4k
views
KEGGgraph question
Pathways KEGGgraph Pathways KEGGgraph
16.2 years ago • updated 16.1 years ago Sim, Fraser ▴ 350
0
votes
0
replies
1.1k
views
KEGGgraph ??
Pathways GO GOstats keggorth KEGGgraph Pathways GO GOstats keggorth KEGGgraph
16.6 years ago Paul Evans ▴ 180
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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