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Showing :
keggrest
•
reset
0
votes
0
replies
333
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
933
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
962
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
884
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 7.2 years ago by
Gordon Smyth
50k • written 7.2 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: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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