Showing : keggrest • reset
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
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 25k • written 5.9 years ago by ▴ 10
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 3.8k • written 6.2 years ago by ▴ 10
2
votes
15
replies
3.8k
views
Timeout error in kegga() using edgeR
edger kegga keggrest
8.3 years ago Likai Mao ▴ 40
2
votes
1
reply
1.4k
views
Possible bug: outdated result from listDatabases()
KEGGREST bug
updated 6.7 years ago by ▴ 50 • written 6.7 years ago by • 0
2
votes
1
reply
965
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
1
vote
8
replies
1.9k
views
KEGGREST mapping between genes and pathways
keggrest mapping genes to pathways
updated 5.2 years ago by 50k • written 5.2 years ago by ▴ 10
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 • 0
1
vote
1
reply
1.2k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 12 months ago by ★ 3.9k • written 12 months ago by • 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 ▴ 10 • written 6.0 years ago by ▴ 20
1
vote
1
reply
1.4k
views
KEGGREST fail to fetch human genes link to pathway
keggrest clusterProfiler
updated 8.7 years ago by ★ 8.2k • written 8.7 years ago by ★ 1.2k
0
votes
2
replies
3.1k
views
Get the reactions for a organism using KEGGREST
keggrest
7.9 years ago kjboteroo • 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
2.2k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 7.3 years ago by 50k • written 7.3 years ago by • 0
0
votes
1
reply
826
views
KEGGSOAP:: KEGGxmlns object not found
keggsoap keggrest
5.9 years ago doctor.dee005 • 0
0
votes
2
replies
888
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 4.0 years ago by 25k • written 4.0 years ago by • 0
0
votes
0
replies
977
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
338
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 months ago mch • 0
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 3.8k • written 22 months ago by ★ 2.0k
0
votes
1
reply
55
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 12 hours ago by ▴ 30 • written 15 hours ago by • 0
0
votes
3
replies
937
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
20 months ago abf ▴ 30
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
2
replies
1.5k
views
keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL KEGGREST
14 months ago jonathanlecoy • 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
11.1 years ago Tarca, Adi ▴ 570
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 ▴ 470 • written 10.6 years ago by ▴ 660
0
votes
1
reply
1.8k
views
trouble reading DNA stringset from keggGet function
PROcess KEGGREST PROcess KEGGREST
updated 10.6 years ago by 65k • written 10.6 years ago by ★ 13k
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
1.5k
views
Error message using arrayweights
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST
updated 10.3 years ago by ▴ 1000 • written 10.3 years ago by ▴ 80
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 65k • written 10.3 years ago by ★ 13k
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 41k • written 9.9 years ago by ▴ 50
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 65k • written 9.4 years ago by ▴ 100
0
votes
1
reply
1.6k
views
Problem in KEGGREST package function keggConv
KEGGREST keggConv
updated 8.2 years ago by ★ 8.2k • written 8.2 years ago by ▴ 120
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
34 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
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
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