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KEGGREST
•
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0
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0
replies
296
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
14 months ago
jol.espinoz
▴ 40
2
votes
1
reply
310
views
GSEA generate genesets
pathway
KEGGREST
GSEA
updated 14 months ago by
Kevin Blighe
3.5k • written 14 months ago by
MOHAMMAD
• 0
0
votes
1
reply
330
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 2.1 years ago by
Martin Morgan
25k • written 2.1 years ago by
predeus
• 0
0
votes
2
replies
359
views
how can I find a pathway
kegg
KEGGREST
2.5 years ago
Bioinformatics
▴ 30
1
vote
8
replies
776
views
KEGGREST mapping between genes and pathways
keggrest
mapping genes to pathways
updated 3.3 years ago by
Gordon Smyth
45k • written 3.3 years ago by
zhang.jianhai
• 0
3
votes
4
replies
2.3k
views
How i can get a list of KEGG pathways and its list of genes?
keggrest
updated 3.9 years ago by
Martin Morgan
25k • written 4.0 years ago by
malik.yousef
▴ 10
0
votes
1
reply
388
views
KEGGSOAP:: KEGGxmlns object not found
keggsoap
keggrest
4.0 years ago
doctor.dee005
• 0
1
vote
9
replies
1.4k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG
keggrest
updated 4.1 years ago by
7kemZmani
▴ 10 • written 4.1 years ago by
hkarakurt
▴ 20
1
vote
4
replies
1.1k
views
How do I convert kegg info on drug to a format allowing me to calculate similarities?
keggrest
chemminer
fmcsr
graph
updated 4.2 years ago by
jennietodd141
• 0 • written 4.2 years ago by
Joris.Meys
• 0
2
votes
1
reply
543
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest
biostrings
updated 4.3 years ago by
shepherl
3.1k • written 4.3 years ago by
xieduo
▴ 10
2
votes
1
reply
983
views
Possible bug: outdated result from listDatabases()
KEGGREST
bug
updated 4.8 years ago by
daniel.vantwisk
▴ 50 • written 4.8 years ago by
olj23
• 0
0
votes
2
replies
894
views
Accessing KEGG (errors w/ KEGGREST)
KEGG
keggrest
updated 5.3 years ago by
Gordon Smyth
45k • written 5.3 years ago by
sampsonj74
• 0
0
votes
2
replies
901
views
Retrieve KEGG from protein GI
R
KEGG
KEGGREST
5.4 years ago
felipelira3
• 0
0
votes
2
replies
1.7k
views
Get the reactions for a organism using KEGGREST
keggrest
6.0 years ago
kjboteroo
• 0
0
votes
11
replies
2.9k
views
Examples from keggList in KEGGREST don't all work
software error
keggrest
6.2 years ago
Bryan Hanson
• 0
0
votes
1
reply
1.0k
views
Problem in KEGGREST package function keggConv
KEGGREST
keggConv
updated 6.3 years ago by
Dan Tenenbaum
★ 8.2k • written 6.3 years ago by
Asta Laiho
▴ 120
2
votes
15
replies
2.4k
views
Timeout error in kegga() using edgeR
edger
kegga
keggrest
6.4 years ago
Likai Mao
▴ 30
1
vote
1
reply
943
views
KEGGREST fail to fetch human genes link to pathway
keggrest
clusterProfiler
updated 6.7 years ago by
Dan Tenenbaum
★ 8.2k • written 6.7 years ago by
Guangchuang Yu
★ 1.2k
0
votes
2
replies
5.8k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest
kegg
keggorthology
updated 7.5 years ago by
James W. MacDonald
59k • written 7.5 years ago by
francesca.defilippis
▴ 80
0
votes
4
replies
2.2k
views
Error: could not find function "plotPCA"
GO
affycoretools
KEGGREST
GO
affycoretools
KEGGREST
updated 8.0 years ago by
Michael Love
37k • written 8.0 years ago by
Surles, Monique
▴ 50
0
votes
1
reply
1.1k
views
limma2annaffy
GO
GUI
annaffy
oligo
oligoClasses
KEGGREST
GO
GUI
annaffy
oligo
oligoClasses
KEGGREST
updated 8.4 years ago by
James W. MacDonald
59k • written 8.4 years ago by
Guest User
★ 12k
0
votes
1
reply
1.1k
views
Error message using arrayweights
GO
Cancer
mouse4302
KEGGREST
GO
Cancer
mouse4302
KEGGREST
updated 8.4 years ago by
Matthew Ritchie
▴ 1000 • written 8.4 years ago by
Richard Friedman
▴ 80
0
votes
0
replies
1.2k
views
Pathview question
KEGGREST
pathview
KEGGREST
pathview
8.7 years ago
Luo Weijun
★ 1.5k
0
votes
1
reply
1.1k
views
trouble reading DNA stringset from keggGet function
PROcess
KEGGREST
PROcess
KEGGREST
updated 8.7 years ago by
James W. MacDonald
59k • written 8.7 years ago by
Guest User
★ 12k
0
votes
7
replies
3.8k
views
Simple pathway enrichment analysis for gene lists
Microarray
Category
gage
KEGGREST
ROntoTools
Microarray
Category
gage
KEGGREST
ROntoTools
updated 8.7 years ago by
Paul Shannon
▴ 470 • written 8.7 years ago by
enricoferrero
▴ 610
0
votes
0
replies
1.2k
views
SPIA algorithm organisms not included already in the SPIA package
Organism
SPIA
goseq
KEGGREST
Organism
SPIA
goseq
KEGGREST
9.2 years ago
Tarca, Adi
▴ 570
0
votes
0
replies
735
views
KEGGREST package is available in devel
KEGGSOAP
KEGGREST
KEGGSOAP
KEGGREST
9.4 years ago
Dan Tenenbaum
★ 8.2k
27 results • Page
1 of 1
Recent ...
Replies
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
Michael Love
37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
andrebolerbarros
▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Awards
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to
Gordon Smyth
45k
Popular Question
to
andrebolerbarros
▴ 10
Scholar
to
James W. MacDonald
59k
Scholar
to
Guido Hooiveld
★ 3.2k
Scholar
to
Kevin Blighe
3.5k
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