Showing : KEGGREST • reset
4
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Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 30
0
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0
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675
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
18 months ago mch • 0
1
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1
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2.8k
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Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by ▴ 10
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2
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2.3k
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keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL KEGGREST
2.2 years ago jonathanlecoy • 0
3
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13
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3.6k
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pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.7 years ago • updated 2.2 years ago nute11a ▴ 10
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3
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1.4k
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ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.7 years ago abf ▴ 30
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3
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2.9k
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Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 2.8 years ago by 4.1k • written 2.8 years ago by ★ 2.0k
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0
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1.4k
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How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
4.1 years ago jol.espinoz ▴ 40
2
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1
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1.2k
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GSEA generate genesets
pathway KEGGREST GSEA
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
0
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1
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2.4k
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KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
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2
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1.2k
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how can I find a pathway
kegg KEGGREST
5.4 years ago Bioinformatics ▴ 30
1
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8
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2.5k
views
KEGGREST mapping between genes and pathways
keggrest mapping genes to pathways
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 10
3
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4
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13k
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How i can get a list of KEGG pathways and its list of genes?
keggrest
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 10
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1
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1.0k
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KEGGSOAP:: KEGGxmlns object not found
keggsoap keggrest
6.9 years ago doctor.dee005 • 0
1
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9
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3.6k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 7.0 years ago by ▴ 10 • written 7.0 years ago by ▴ 20
1
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4
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2.6k
views
How do I convert kegg info on drug to a format allowing me to calculate similarities?
keggrest chemminer fmcsr graph
written 7.1 years ago by • 0
2
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1
reply
1.2k
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 7.3 years ago by 4.1k • written 7.3 years ago by ▴ 10
2
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1
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1.7k
views
Possible bug: outdated result from listDatabases()
KEGGREST bug
updated 7.7 years ago by ▴ 50 • written 7.7 years ago by • 0
0
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2
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3.4k
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Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 8.3 years ago by 52k • written 8.3 years ago by • 0
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2
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1.5k
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Retrieve KEGG from protein GI
R KEGG KEGGREST
8.4 years ago felipelira3 • 0
0
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2
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3.7k
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Get the reactions for a organism using KEGGREST
keggrest
9.0 years ago • updated 8.9 years ago kjboteroo • 0
0
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11
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5.6k
views
Examples from keggList in KEGGREST don't all work
software error keggrest
9.1 years ago Bryan Hanson • 0
0
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1
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2.0k
views
Problem in KEGGREST package function keggConv
KEGGREST keggConv
updated 9.2 years ago by ★ 8.2k • written 9.2 years ago by ▴ 120
2
votes
15
replies
4.7k
views
Timeout error in kegga() using edgeR
edger kegga keggrest
9.3 years ago Likai Mao ▴ 40
1
vote
1
reply
1.7k
views
KEGGREST fail to fetch human genes link to pathway
keggrest clusterProfiler
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by ★ 1.2k
0
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2
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8.6k
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Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 10.4 years ago by 68k • written 10.4 years ago by ▴ 100
0
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4
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3.3k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 50
0
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1
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1.7k
views
limma2annaffy
GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST
updated 11.3 years ago by 68k • written 11.3 years ago by ★ 13k
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1
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1.7k
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Error message using arrayweights
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST
updated 11.4 years ago by ▴ 1000 • written 11.4 years ago by ▴ 80
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0
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1.9k
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Pathview question
KEGGREST pathview KEGGREST pathview
11.6 years ago Luo Weijun ★ 1.6k
0
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1
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2.1k
views
trouble reading DNA stringset from keggGet function
PROcess KEGGREST PROcess KEGGREST
updated 11.6 years ago by 68k • written 11.6 years ago by ★ 13k
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7
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5.3k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 11.6 years ago by ▴ 470 • written 11.6 years ago by ▴ 680
0
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0
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1.9k
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SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
12.2 years ago Tarca, Adi ▴ 570
0
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0
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1.3k
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KEGGREST package is available in devel
KEGGSOAP KEGGREST KEGGSOAP KEGGREST
12.3 years ago Dan Tenenbaum ★ 8.2k
34 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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