Showing : keggrest • reset
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 months ago mch • 0
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1
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1.2k
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Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 12 months ago by ★ 3.9k • written 12 months ago by • 0
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2
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1.5k
views
keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL KEGGREST
14 months ago jonathanlecoy • 0
3
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13
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2.5k
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pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 14 months ago nute11a ▴ 10
0
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3
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936
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ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
20 months ago abf ▴ 30
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3
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1.9k
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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
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976
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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
3.1 years ago jol.espinoz ▴ 40
2
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1
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964
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
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1.7k
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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
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886
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how can I find a pathway
kegg KEGGREST
4.4 years ago Bioinformatics ▴ 30
1
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1.9k
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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
3
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4
replies
8.2k
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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
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826
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KEGGSOAP:: KEGGxmlns object not found
keggsoap keggrest
5.9 years ago doctor.dee005 • 0
1
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9
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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
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4
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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
2
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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
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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
0
votes
2
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2.2k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 7.3 years ago by 50k • written 7.3 years ago by • 0
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2
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1.3k
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Retrieve KEGG from protein GI
R KEGG KEGGREST
7.3 years ago felipelira3 • 0
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2
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3.1k
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Get the reactions for a organism using KEGGREST
keggrest
7.9 years ago kjboteroo • 0
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11
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4.3k
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Examples from keggList in KEGGREST don't all work
software error keggrest
8.1 years ago Bryan Hanson • 0
0
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1
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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
2
votes
15
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3.8k
views
Timeout error in kegga() using edgeR
edger kegga keggrest
8.3 years ago Likai Mao ▴ 40
1
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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
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2
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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
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
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1
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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
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1
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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
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0
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1.6k
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Pathview question
KEGGREST pathview KEGGREST pathview
10.6 years ago Luo Weijun ★ 1.6k
0
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1
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1.8k
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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
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7
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4.7k
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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
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0
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1.7k
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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
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0
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1.1k
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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: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
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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