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KEGGREST
•
reset
2
votes
15
replies
3.9k
views
Timeout error in kegga() using edgeR
edger
kegga
keggrest
8.3 years ago
Likai Mao
▴ 40
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
James W. MacDonald
65k • written 9.5 years ago by
francesca.defilippis
▴ 100
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
7kemZmani
▴ 10 • written 6.1 years ago by
hkarakurt
▴ 20
3
votes
4
replies
8.4k
views
How i can get a list of KEGG pathways and its list of genes?
keggrest
updated 5.9 years ago by
Martin Morgan
25k • written 5.9 years ago by
malik.yousef
▴ 10
0
votes
3
replies
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
shepherl
3.9k • written 22 months ago by
Jenny Drnevich
★ 2.0k
1
vote
4
replies
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
Joris.Meys
• 0
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
0
votes
1
reply
1.6k
views
Problem in KEGGREST package function keggConv
KEGGREST
keggConv
updated 8.3 years ago by
Dan Tenenbaum
★ 8.2k • written 8.3 years ago by
Asta Laiho
▴ 120
0
votes
2
replies
3.1k
views
Get the reactions for a organism using KEGGREST
keggrest
8.0 years ago
kjboteroo
• 0
0
votes
2
replies
2.3k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG
keggrest
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
sampsonj74
• 0
2
votes
1
reply
1.5k
views
Possible bug: outdated result from listDatabases()
KEGGREST
bug
updated 6.7 years ago by
daniel.vantwisk
▴ 50 • written 6.7 years ago by
olj23
• 0
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
shepherl
3.9k • written 6.3 years ago by
xieduo
▴ 10
0
votes
2
replies
1.5k
views
keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL
KEGGREST
14 months ago
jonathanlecoy
• 0
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
Paul Shannon
▴ 470 • written 10.7 years ago by
enricoferrero
▴ 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
James W. MacDonald
65k • written 10.7 years ago by
Guest User
★ 13k
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
Matthew Ritchie
▴ 1000 • written 10.4 years ago by
Richard Friedman
▴ 80
0
votes
1
reply
1.5k
views
limma2annaffy
GO
GUI
annaffy
oligo
oligoClasses
KEGGREST
GO
GUI
annaffy
oligo
oligoClasses
KEGGREST
updated 10.4 years ago by
James W. MacDonald
65k • written 10.4 years ago by
Guest User
★ 13k
0
votes
4
replies
2.9k
views
Error: could not find function "plotPCA"
GO
affycoretools
KEGGREST
GO
affycoretools
KEGGREST
updated 10.0 years ago by
Michael Love
41k • written 10.0 years ago by
Surles, Monique
▴ 50
1
vote
1
reply
1.4k
views
KEGGREST fail to fetch human genes link to pathway
keggrest
clusterProfiler
updated 8.7 years ago by
Dan Tenenbaum
★ 8.2k • written 8.7 years ago by
Guangchuang Yu
★ 1.2k
1
vote
8
replies
2.0k
views
KEGGREST mapping between genes and pathways
keggrest
mapping genes to pathways
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
zhang.jianhai
▴ 10
2
votes
1
reply
979
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
MOHAMMAD
• 0
1
vote
1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 12 months ago by
Guido Hooiveld
★ 3.9k • written 12 months ago by
morgan.sobol
• 0
3
votes
2
replies
214
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 13 days ago by
Guido Hooiveld
★ 3.9k • written 16 days ago by
fernanda.backsouza
▴ 10
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
Martin Morgan
25k • written 4.1 years ago by
predeus
• 0
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
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
votes
0
replies
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
replies
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
1.7k
views
Pathview question
KEGGREST
pathview
KEGGREST
pathview
10.6 years ago
Luo Weijun
★ 1.6k
0
votes
2
replies
1.3k
views
Retrieve KEGG from protein GI
R
KEGG
KEGGREST
7.4 years ago
felipelira3
• 0
0
votes
1
reply
834
views
KEGGSOAP:: KEGGxmlns object not found
keggsoap
keggrest
6.0 years ago
doctor.dee005
• 0
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
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
34 results • Page
1 of 1
Recent ...
Replies
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)*…
Comment: fgsea significant result
by
Chris
• 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
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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