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keggrest
•
reset
0
votes
0
replies
311
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
1.1k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 11 months ago by
Guido Hooiveld
★ 3.9k • written 11 months ago by
morgan.sobol
• 0
0
votes
2
replies
1.4k
views
keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL
KEGGREST
13 months ago
jonathanlecoy
• 0
3
votes
13
replies
2.4k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
19 months ago • updated 13 months ago
nute11a
▴ 10
0
votes
3
replies
908
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
1.8k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma
KEGGREST
EGSEA
updated 21 months ago by
shepherl
3.8k • written 21 months ago by
Jenny Drnevich
★ 2.0k
0
votes
0
replies
950
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
3.0 years ago
jol.espinoz
▴ 40
2
votes
1
reply
943
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 3.0 years ago by
Kevin Blighe
★ 3.9k • written 3.0 years ago by
MOHAMMAD
• 0
0
votes
1
reply
1.6k
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
868
views
how can I find a pathway
kegg
KEGGREST
4.3 years ago
Bioinformatics
▴ 30
1
vote
8
replies
1.9k
views
KEGGREST mapping between genes and pathways
keggrest
mapping genes to pathways
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
zhang.jianhai
▴ 10
3
votes
4
replies
7.9k
views
How i can get a list of KEGG pathways and its list of genes?
keggrest
updated 5.8 years ago by
Martin Morgan
25k • written 5.8 years ago by
malik.yousef
▴ 10
0
votes
1
reply
820
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
2.0k
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
923
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 6.6 years ago by
daniel.vantwisk
▴ 50 • written 6.6 years ago by
olj23
• 0
0
votes
2
replies
2.2k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG
keggrest
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
sampsonj74
• 0
0
votes
2
replies
1.2k
views
Retrieve KEGG from protein GI
R
KEGG
KEGGREST
7.3 years ago
felipelira3
• 0
0
votes
2
replies
3.0k
views
Get the reactions for a organism using KEGGREST
keggrest
7.9 years ago
kjboteroo
• 0
0
votes
11
replies
4.2k
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
8.2 years ago
Likai Mao
▴ 40
1
vote
1
reply
1.4k
views
KEGGREST fail to fetch human genes link to pathway
keggrest
clusterProfiler
updated 8.6 years ago by
Dan Tenenbaum
★ 8.2k • written 8.6 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
1.4k
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
10.5 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.7k
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
11.2 years ago
Dan Tenenbaum
★ 8.2k
33 results • Page
1 of 1
Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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