Showing : keggrest • reset
4
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566
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 30
0
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0
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593
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
14 months ago mch • 0
1
vote
1
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2.2k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 21 months ago by ★ 4.1k • written 21 months ago by ▴ 10
0
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2
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2.1k
views
keggList curl::curl_fetch_memory(url, handle = handle) ERROR
URL KEGGREST
23 months ago jonathanlecoy • 0
3
votes
13
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3.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.4 years ago • updated 23 months ago nute11a ▴ 10
0
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3
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1.3k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.5 years ago abf ▴ 30
0
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3
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2.6k
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 2.6 years ago by 4.1k • written 2.6 years ago by ★ 2.0k
0
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0
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1.3k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.8 years ago jol.espinoz ▴ 40
2
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1
reply
1.2k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
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1
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2.2k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
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2
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1.1k
views
how can I find a pathway
kegg KEGGREST
5.2 years ago Bioinformatics ▴ 30
1
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8
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2.3k
views
KEGGREST mapping between genes and pathways
keggrest mapping genes to pathways
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 10
3
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4
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11k
views
How i can get a list of KEGG pathways and its list of genes?
keggrest
updated 6.6 years ago by 25k • written 6.6 years ago by ▴ 10
0
votes
1
reply
961
views
KEGGSOAP:: KEGGxmlns object not found
keggsoap keggrest
6.7 years ago doctor.dee005 • 0
1
vote
9
replies
3.4k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 6.8 years ago by ▴ 10 • written 6.8 years ago by ▴ 20
1
vote
4
replies
2.5k
views
How do I convert kegg info on drug to a format allowing me to calculate similarities?
keggrest chemminer fmcsr graph
written 6.9 years ago by • 0
2
votes
1
reply
1.1k
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 7.0 years ago by 4.1k • written 7.0 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Possible bug: outdated result from listDatabases()
KEGGREST bug
updated 7.5 years ago by ▴ 50 • written 7.5 years ago by • 0
0
votes
2
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3.0k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 8.0 years ago by 52k • written 8.0 years ago by • 0
0
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2
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1.4k
views
Retrieve KEGG from protein GI
R KEGG KEGGREST
8.1 years ago felipelira3 • 0
0
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2
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3.5k
views
Get the reactions for a organism using KEGGREST
keggrest
8.7 years ago kjboteroo • 0
0
votes
11
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5.2k
views
Examples from keggList in KEGGREST don't all work
software error keggrest
8.9 years ago Bryan Hanson • 0
0
votes
1
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1.9k
views
Problem in KEGGREST package function keggConv
KEGGREST keggConv
updated 9.0 years ago by ★ 8.2k • written 9.0 years ago by ▴ 120
2
votes
15
replies
4.5k
views
Timeout error in kegga() using edgeR
edger kegga keggrest
9.1 years ago • updated 9.0 years ago Likai Mao ▴ 40
1
vote
1
reply
1.6k
views
KEGGREST fail to fetch human genes link to pathway
keggrest clusterProfiler
updated 9.4 years ago by ★ 8.2k • written 9.4 years ago by ★ 1.2k
0
votes
2
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8.2k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 10.2 years ago by 67k • written 10.2 years ago by ▴ 100
0
votes
4
replies
3.2k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 10.7 years ago by 43k • written 10.7 years ago by ▴ 50
0
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1
reply
1.7k
views
limma2annaffy
GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST
updated 11.1 years ago by 67k • written 11.1 years ago by ★ 13k
0
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1
reply
1.7k
views
Error message using arrayweights
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST
updated 11.1 years ago by ▴ 1000 • written 11.1 years ago by ▴ 80
0
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0
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1.8k
views
Pathview question
KEGGREST pathview KEGGREST pathview
11.3 years ago Luo Weijun ★ 1.6k
0
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1
reply
2.0k
views
trouble reading DNA stringset from keggGet function
PROcess KEGGREST PROcess KEGGREST
updated 11.4 years ago by 67k • written 11.4 years ago by ★ 13k
0
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7
replies
5.1k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 11.4 years ago by ▴ 470 • written 11.4 years ago by ▴ 660
0
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0
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1.9k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
11.9 years ago Tarca, Adi ▴ 570
0
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0
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1.3k
views
KEGGREST package is available in devel
KEGGSOAP KEGGREST KEGGSOAP KEGGREST
12.0 years ago Dan Tenenbaum ★ 8.2k
34 results • Page 1 of 1
Recent ...
Replies
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?
Answer: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounde…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by alserg ▴ 280
`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…
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