Showing : kegg • reset
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KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
6 weeks ago Jessica • 0
0
votes
2
replies
550
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
8 weeks ago • updated 5 weeks ago ingrid.h • 0
1
vote
4
replies
520
views
pathview - multiple states
pathview Pathways KEGG
3 months ago Philippine • 0
1
vote
2
replies
472
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 6 months ago by ▴ 60 • written 6 months ago by • 0
0
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0
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386
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
8 months ago cereyredondo • 0
0
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3
replies
885
views
pathview error
KEGGgraph KEGG
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
0
replies
325
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
10 months ago danalvoronov ▴ 10
1
vote
1
reply
466
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 11 months ago by 68k • written 11 months ago by ▴ 30
5
votes
13
replies
2.9k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
11 months ago fernanda.backsouza ▴ 30
4
votes
2
replies
650
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 11 months ago by ★ 4.1k • written 11 months ago by ▴ 30
2
votes
4
replies
1.5k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 11 months ago by • 0
2
votes
2
replies
576
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Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
0
replies
652
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
17 months ago mch • 0
0
votes
4
replies
3.0k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 5 months ago by • 0 • written 18 months ago by • 0
3
votes
2
replies
2.3k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 10
0
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0
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603
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
20 months ago georgii.vdovin • 0
1
vote
4
replies
1.7k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
21 months ago Jiyoung Lee • 0
0
votes
1
reply
844
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
0
votes
5
replies
2.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
23 months ago • updated 22 months ago ruba-mahmoud • 0
1
vote
3
replies
1.9k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 23 months ago by ★ 4.1k • written 24 months ago by ▴ 10
0
votes
13
replies
10k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.0 years ago Laia ▴ 10
0
votes
5
replies
1.9k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.0 years ago by • 0
4
votes
11
replies
4.4k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 22 months ago by • 0 • written 2.0 years ago by ▴ 10
4
votes
2
replies
6.5k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 2.1 years ago by ▴ 50 • written 2.1 years ago by • 0
1
vote
7
replies
3.2k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by ▴ 10
2
votes
6
replies
3.8k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 14 months ago by ★ 4.1k • written 2.1 years ago by ▴ 10
1
vote
3
replies
1.7k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
4
votes
2
replies
4.0k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.4 years ago Wuschel ▴ 10
0
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2
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983
views
Shivani
kegg
updated 2.4 years ago by ▴ 60 • written 2.4 years ago by • 0
4
votes
6
replies
5.0k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.6 years ago by ★ 4.1k • written 2.8 years ago by ▴ 10
3
votes
13
replies
3.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.6 years ago • updated 2.1 years ago nute11a ▴ 10
0
votes
3
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1.3k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.6 years ago abf ▴ 30
1
vote
1
reply
1.6k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 20
0
votes
2
replies
1.2k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 2.7 years ago by ▴ 70 • written 2.7 years ago by ▴ 20
1
vote
3
replies
2.7k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 13 months ago by • 0 • written 2.8 years ago by • 0
0
votes
2
replies
3.9k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.8 years ago by ★ 4.0k • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
1
reply
1.7k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
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0
replies
1.1k
views
Editing KEGG pathways in R
KEGG
3.4 years ago Jordan • 0
1
vote
0
replies
1.9k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
3.4 years ago makrez ▴ 10
1
vote
0
replies
1.7k
views
documentation on clusterProfiler output
clusterProfiler KEGG
3.5 years ago rafaela.perez ▴ 10
0
votes
6
replies
5.3k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.6 years ago Bogdan ▴ 670
0
votes
3
replies
2.6k
views
Drawing custom KEGG pathways
pathview KEGG
written 3.8 years ago by ▴ 10
0
votes
2
replies
2.7k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
votes
0
replies
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
4.0 years ago jol.espinoz ▴ 40
6
votes
5
replies
2.0k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.0 years ago by ★ 1.6k • written 4.0 years ago by • 0
2
votes
2
replies
1.5k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
3
replies
1.4k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 670
0
votes
1
reply
2.4k
views
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
2
votes
2
replies
1.6k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k
Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
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Answer: Explannation for ROAST results
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
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