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Showing :
keggrest
•
reset
0
votes
0
replies
336
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
5 months ago
mch
• 0
1
vote
1
reply
1.2k
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
0
votes
2
replies
1.5k
views
keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL
KEGGREST
14 months ago
jonathanlecoy
• 0
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
20 months ago • updated 14 months ago
nute11a
▴ 10
0
votes
3
replies
935
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
20 months ago
abf
▴ 30
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
3.8k • written 22 months ago by
Jenny Drnevich
★ 2.0k
0
votes
0
replies
975
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
2
votes
1
reply
964
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
0
votes
1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
predeus
• 0
0
votes
2
replies
885
views
how can I find a pathway
kegg
KEGGREST
4.4 years ago
Bioinformatics
▴ 30
1
vote
8
replies
1.9k
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
3
votes
4
replies
8.2k
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
1
reply
826
views
KEGGSOAP:: KEGGxmlns object not found
keggsoap
keggrest
5.9 years ago
doctor.dee005
• 0
1
vote
9
replies
2.8k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG
keggrest
updated 6.0 years ago by
7kemZmani
▴ 10 • written 6.0 years ago by
hkarakurt
▴ 20
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 6.1 years ago by
Joris.Meys
• 0
2
votes
1
reply
936
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest
biostrings
updated 6.2 years ago by
shepherl
3.8k • written 6.2 years ago by
xieduo
▴ 10
2
votes
1
reply
1.4k
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
0
votes
2
replies
2.2k
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
0
votes
2
replies
1.3k
views
Retrieve KEGG from protein GI
R
KEGG
KEGGREST
7.3 years ago
felipelira3
• 0
0
votes
2
replies
3.1k
views
Get the reactions for a organism using KEGGREST
keggrest
7.9 years ago
kjboteroo
• 0
0
votes
11
replies
4.3k
views
Examples from keggList in KEGGREST don't all work
software error
keggrest
8.1 years ago
Bryan Hanson
• 0
0
votes
1
reply
1.6k
views
Problem in KEGGREST package function keggConv
KEGGREST
keggConv
updated 8.2 years ago by
Dan Tenenbaum
★ 8.2k • written 8.2 years ago by
Asta Laiho
▴ 120
2
votes
15
replies
3.8k
views
Timeout error in kegga() using edgeR
edger
kegga
keggrest
8.3 years ago
Likai Mao
▴ 40
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
0
votes
2
replies
7.3k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest
kegg
keggorthology
updated 9.4 years ago by
James W. MacDonald
65k • written 9.4 years ago by
francesca.defilippis
▴ 100
0
votes
4
replies
2.9k
views
Error: could not find function "plotPCA"
GO
affycoretools
KEGGREST
GO
affycoretools
KEGGREST
updated 9.9 years ago by
Michael Love
41k • written 9.9 years ago by
Surles, Monique
▴ 50
0
votes
1
reply
1.5k
views
limma2annaffy
GO
GUI
annaffy
oligo
oligoClasses
KEGGREST
GO
GUI
annaffy
oligo
oligoClasses
KEGGREST
updated 10.3 years ago by
James W. MacDonald
65k • written 10.3 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 10.3 years ago by
Matthew Ritchie
▴ 1000 • written 10.3 years ago by
Richard Friedman
▴ 80
0
votes
0
replies
1.6k
views
Pathview question
KEGGREST
pathview
KEGGREST
pathview
10.6 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.8k
views
trouble reading DNA stringset from keggGet function
PROcess
KEGGREST
PROcess
KEGGREST
updated 10.6 years ago by
James W. MacDonald
65k • written 10.6 years ago by
Guest User
★ 13k
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 10.6 years ago by
Paul Shannon
▴ 470 • written 10.6 years ago by
enricoferrero
▴ 660
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
11.1 years ago
Tarca, Adi
▴ 570
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
33 results • Page
1 of 1
Recent ...
Replies
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR
by
Gordon Smyth
50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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