Showing : KEGGREST • reset
3
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4
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8.4k
views
How i can get a list of KEGG pathways and its list of genes?
keggrest
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 10
3
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2
replies
214
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 13 days ago by ★ 3.9k • written 16 days ago by ▴ 10
3
votes
13
replies
2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 15 months ago nute11a ▴ 10
2
votes
1
reply
979
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
2
votes
15
replies
3.9k
views
Timeout error in kegga() using edgeR
edger kegga keggrest
8.3 years ago Likai Mao ▴ 40
2
votes
1
reply
948
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 6.3 years ago by 3.9k • written 6.3 years ago by ▴ 10
2
votes
1
reply
1.5k
views
Possible bug: outdated result from listDatabases()
KEGGREST bug
updated 6.7 years ago by ▴ 50 • written 6.7 years ago by • 0
1
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1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 12 months ago by ★ 3.9k • written 12 months ago by • 0
1
vote
1
reply
1.4k
views
KEGGREST fail to fetch human genes link to pathway
keggrest clusterProfiler
updated 8.7 years ago by ★ 8.2k • written 8.7 years ago by ★ 1.2k
1
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4
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2.1k
views
How do I convert kegg info on drug to a format allowing me to calculate similarities?
keggrest chemminer fmcsr graph
written 6.2 years ago by • 0
1
vote
8
replies
2.0k
views
KEGGREST mapping between genes and pathways
keggrest mapping genes to pathways
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 10
1
vote
9
replies
2.9k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by ▴ 20
0
votes
2
replies
1.3k
views
Retrieve KEGG from protein GI
R KEGG KEGGREST
7.4 years ago felipelira3 • 0
0
votes
2
replies
2.3k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 7.3 years ago by 50k • written 7.3 years ago by • 0
0
votes
1
reply
834
views
KEGGSOAP:: KEGGxmlns object not found
keggsoap keggrest
6.0 years ago doctor.dee005 • 0
0
votes
2
replies
901
views
how can I find a pathway
kegg KEGGREST
4.4 years ago Bioinformatics ▴ 30
0
votes
1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.1 years ago by 25k • written 4.1 years ago by • 0
0
votes
0
replies
996
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.1 years ago jol.espinoz ▴ 40
0
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0
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355
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
0
votes
3
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1.9k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 22 months ago by 3.9k • written 22 months ago by ★ 2.0k
0
votes
3
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953
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
21 months ago abf ▴ 30
0
votes
0
replies
1.1k
views
KEGGREST package is available in devel
KEGGSOAP KEGGREST KEGGSOAP KEGGREST
11.3 years ago Dan Tenenbaum ★ 8.2k
0
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2
replies
1.5k
views
keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL KEGGREST
14 months ago jonathanlecoy • 0
0
votes
0
replies
1.7k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
11.2 years ago Tarca, Adi ▴ 570
0
votes
7
replies
4.7k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 10.7 years ago by ▴ 470 • written 10.7 years ago by ▴ 660
0
votes
1
reply
1.8k
views
trouble reading DNA stringset from keggGet function
PROcess KEGGREST PROcess KEGGREST
updated 10.7 years ago by 65k • written 10.7 years ago by ★ 13k
0
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0
replies
1.7k
views
Pathview question
KEGGREST pathview KEGGREST pathview
10.6 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.5k
views
Error message using arrayweights
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST
updated 10.4 years ago by ▴ 1000 • written 10.4 years ago by ▴ 80
0
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1
reply
1.5k
views
limma2annaffy
GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST
updated 10.4 years ago by 65k • written 10.4 years ago by ★ 13k
0
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4
replies
2.9k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 10.0 years ago by 41k • written 10.0 years ago by ▴ 50
0
votes
2
replies
7.4k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 100
0
votes
1
reply
1.6k
views
Problem in KEGGREST package function keggConv
KEGGREST keggConv
updated 8.3 years ago by ★ 8.2k • written 8.3 years ago by ▴ 120
0
votes
11
replies
4.4k
views
Examples from keggList in KEGGREST don't all work
software error keggrest
8.2 years ago Bryan Hanson • 0
0
votes
2
replies
3.1k
views
Get the reactions for a organism using KEGGREST
keggrest
8.0 years ago kjboteroo • 0
34 results • Page 1 of 1
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Replies
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 with no issues at all. If you're having trouble with Bioc installa…
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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