Showing : kegg • reset
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Student
metaboliteIDmapping Metabolomics KEGG
20 minutes ago vipinsapla • 0
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0
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217
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
9 weeks ago cereyredondo • 0
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3
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417
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pathview error
KEGGgraph KEGG
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
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0
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187
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
4 months ago danalvoronov ▴ 10
1
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1
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291
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Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 4 months ago by 67k • written 4 months ago by ▴ 20
4
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13
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1.5k
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
4 months ago fernanda.backsouza ▴ 20
4
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2
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424
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Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 4 months ago by ★ 4.1k • written 5 months ago by ▴ 20
2
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2
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512
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
5 months ago julia_mcdonough • 0
2
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2
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417
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Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
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0
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500
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
10 months ago mch • 0
0
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3
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1.9k
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pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 11 months ago by ▴ 30 • written 12 months ago by • 0
3
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2
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1.5k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 10
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0
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480
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
14 months ago georgii.vdovin • 0
1
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4
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1.4k
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pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
15 months ago Jiyoung Lee • 0
0
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1
reply
688
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 15 months ago by 42k • written 15 months ago by • 0
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5
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1.7k
views
enrichKEGG function error
cluster clusterProfiler KEGG
17 months ago • updated 16 months ago ruba-mahmoud • 0
1
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3
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1.5k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 17 months ago by ★ 4.1k • written 17 months ago by ▴ 10
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13
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6.6k
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KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
18 months ago Laia ▴ 10
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5
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1.5k
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[limma::kegga] Pathway names all NA
KEGG limma
written 18 months ago by • 0
4
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11
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3.3k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 16 months ago by • 0 • written 18 months ago by ▴ 10
4
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2
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5.2k
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gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 18 months ago by ▴ 50 • written 18 months ago by • 0
1
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7
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2.4k
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Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 18 months ago by ▴ 780 • written 18 months ago by ▴ 10
2
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6
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2.6k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 8 months ago by ★ 4.1k • written 18 months ago by ▴ 10
1
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3
replies
1.4k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 21 months ago by 67k • written 22 months ago by • 0
4
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2
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2.8k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
23 months ago Wuschel ▴ 10
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2
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832
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Shivani
kegg
updated 23 months ago by ▴ 60 • written 23 months ago by • 0
4
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6
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4.2k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.0 years ago by ★ 4.1k • written 2.2 years ago by ▴ 10
3
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13
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3.0k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.1 years ago • updated 19 months ago nute11a ▴ 10
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3
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1.2k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.1 years ago abf ▴ 30
1
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1
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1.4k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 2.1 years ago by 67k • written 2.1 years ago by ▴ 20
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2
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1.0k
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How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 2.1 years ago by ▴ 70 • written 2.1 years ago by ▴ 20
1
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3
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2.2k
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enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 7 months ago by • 0 • written 2.3 years ago by • 0
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2
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3.6k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
0
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1
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973
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
0
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1
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1.4k
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How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.6 years ago by ★ 4.0k • written 2.6 years ago by • 0
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0
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933
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Editing KEGG pathways in R
KEGG
2.9 years ago Jordan • 0
1
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0
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1.5k
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GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.9 years ago makrez ▴ 10
1
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0
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1.4k
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documentation on clusterProfiler output
clusterProfiler KEGG
3.0 years ago rafaela.perez ▴ 10
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6
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4.1k
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extracting the KEGG pathway for a set of genes
Pathways KEGG
3.1 years ago Bogdan ▴ 670
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2
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2.1k
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Drawing custom KEGG pathways
pathview KEGG
3.3 years ago curiousmind007 ▴ 10
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2
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2.4k
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Can't install KEGGprofile
KEGG RNASeq
updated 3.3 years ago by 67k • written 3.3 years ago by • 0
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0
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1.2k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.5 years ago jol.espinoz ▴ 40
6
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5
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1.7k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.5 years ago by ★ 1.6k • written 3.5 years ago by • 0
2
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2
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1.3k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
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3
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1.3k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.3 years ago by 67k • written 4.3 years ago by ▴ 670
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1
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1.9k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.4 years ago by 25k • written 4.4 years ago by • 0
2
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2
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1.3k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.5 years ago by 67k • written 4.5 years ago by ▴ 20
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0
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916
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.5 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
1.3k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 4.6 years ago by 51k • written 5.0 years ago by ▴ 50
6
votes
6
replies
5.4k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.6 years ago by 51k • written 4.6 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: ReactomeGSA adjustment for confounding variables by trangthi19876 • 0
Validation: Validate your findings by checking the robustness of the results across different model specifications and potential interactio…
Comment: Issue Installing Biostrings Package: gcc Compilation Errors by tiffanygrimmet • 0
@[tiny fishing](https://tiny-fishing.com) : You below have made too many mistakes in line 20, you have made quite a few mistakes in line 20…
Comment: How to use compareCluster in ClusterProfiler? by cynthiamoniz1122 • 0
@[poppy playtime chapter 3](https://poppyplaytimechapter3.io): Your code provides quite complete information, you code very detailed and sp…
Comment: Should tSNE from biol. replicates look alike? by cynthiamoniz1122 • 0
good ideal
Answer: Trying to convert ATACseq annotations of non-model species into human orthologs, by James W. MacDonald 67k
I would use the mapper I note above, and build your own `OrgDb`, then do the GO analysis directly. ``` > library(AnnotationForge) > option…
Votes
Answer: Trying to convert ATACseq annotations of non-model species into human orthologs,
Answer: Trying to convert ATACseq annotations of non-model species into human orthologs,
Answer: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
A: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
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