Showing : keggrest • reset
0
votes
13
replies
715
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
5 months ago • updated 8 hours ago nute11a • 0
0
votes
3
replies
335
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
6 months ago abf ▴ 30
0
votes
3
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659
views
Problem in kegga() and others getting data from KEGG after switch from http to https
limma KEGGREST EGSEA
updated 7 months ago by 3.4k • written 7 months ago by ★ 2.0k
0
votes
0
replies
484
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
22 months ago jol.espinoz ▴ 40
2
votes
1
reply
481
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 22 months ago by 3.7k • written 22 months ago by • 0
0
votes
1
reply
712
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 2.8 years ago by 25k • written 2.8 years ago by • 0
0
votes
2
replies
498
views
how can I find a pathway
kegg KEGGREST
3.2 years ago Bioinformatics ▴ 30
1
vote
8
replies
1.2k
views
KEGGREST mapping between genes and pathways
keggrest mapping genes to pathways
updated 4.0 years ago by 47k • written 4.0 years ago by ▴ 10
3
votes
4
replies
3.6k
views
How i can get a list of KEGG pathways and its list of genes?
keggrest
updated 4.6 years ago by 25k • written 4.7 years ago by ▴ 10
0
votes
1
reply
526
views
KEGGSOAP:: KEGGxmlns object not found
keggsoap keggrest
4.7 years ago doctor.dee005 • 0
1
vote
9
replies
1.8k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 4.8 years ago by ▴ 10 • written 4.8 years ago by ▴ 20
1
vote
4
replies
1.4k
views
How do I convert kegg info on drug to a format allowing me to calculate similarities?
keggrest chemminer fmcsr graph
updated 4.9 years ago by • 0 • written 4.9 years ago by • 0
2
votes
1
reply
628
views
How can I remove the ellipsis and get the complete sequence and results?
keggrest biostrings
updated 5.0 years ago by 3.4k • written 5.0 years ago by ▴ 10
2
votes
1
reply
1.1k
views
Possible bug: outdated result from listDatabases()
KEGGREST bug
updated 5.5 years ago by ▴ 50 • written 5.5 years ago by • 0
0
votes
2
replies
1.3k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 6.0 years ago by 47k • written 6.0 years ago by • 0
0
votes
2
replies
979
views
Retrieve KEGG from protein GI
R KEGG KEGGREST
6.1 years ago felipelira3 • 0
0
votes
2
replies
2.1k
views
Get the reactions for a organism using KEGGREST
keggrest
6.7 years ago kjboteroo • 0
0
votes
11
replies
3.2k
views
Examples from keggList in KEGGREST don't all work
software error keggrest
6.9 years ago Bryan Hanson • 0
0
votes
1
reply
1.2k
views
Problem in KEGGREST package function keggConv
KEGGREST keggConv
updated 7.0 years ago by ★ 8.2k • written 7.0 years ago by ▴ 120
2
votes
15
replies
2.8k
views
Timeout error in kegga() using edgeR
edger kegga keggrest
7.1 years ago Likai Mao ▴ 40
1
vote
1
reply
1.1k
views
KEGGREST fail to fetch human genes link to pathway
keggrest clusterProfiler
updated 7.4 years ago by ★ 8.2k • written 7.5 years ago by ★ 1.2k
0
votes
2
replies
6.3k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 8.2 years ago by 62k • written 8.2 years ago by ▴ 80
0
votes
4
replies
2.4k
views
Error: could not find function "plotPCA"
GO affycoretools KEGGREST GO affycoretools KEGGREST
updated 8.7 years ago by 39k • written 8.7 years ago by ▴ 50
0
votes
1
reply
1.2k
views
limma2annaffy
GO GUI annaffy oligo oligoClasses KEGGREST GO GUI annaffy oligo oligoClasses KEGGREST
updated 9.1 years ago by 62k • written 9.1 years ago by ★ 12k
0
votes
1
reply
1.2k
views
Error message using arrayweights
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST
updated 9.1 years ago by ▴ 1000 • written 9.1 years ago by ▴ 80
0
votes
0
replies
1.3k
views
Pathview question
KEGGREST pathview KEGGREST pathview
9.4 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.4k
views
trouble reading DNA stringset from keggGet function
PROcess KEGGREST PROcess KEGGREST
updated 9.4 years ago by 62k • written 9.4 years ago by ★ 12k
0
votes
7
replies
4.1k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 9.4 years ago by ▴ 470 • written 9.4 years ago by ▴ 650
0
votes
0
replies
1.3k
views
SPIA algorithm organisms not included already in the SPIA package
Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST
9.9 years ago Tarca, Adi ▴ 570
0
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0
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835
views
KEGGREST package is available in devel
KEGGSOAP KEGGREST KEGGSOAP KEGGREST
10.1 years ago Dan Tenenbaum ★ 8.2k
30 results • Page 1 of 1
Recent ...
Replies
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by Michael Love 39k
Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…
Votes
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Awards • All
Popular Question to Guido Hooiveld ★ 3.5k
Scholar to James W. MacDonald 62k
Commentator to Michael Love 39k
Popular Question to twtoal ▴ 10
Student to L ▴ 40
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