Showing : kegg • reset
0
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3
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206
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pathview error
KEGGgraph KEGG
updated 25 days ago by ★ 4.0k • written 26 days ago by • 0
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93
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
4 weeks ago danalvoronov ▴ 10
1
vote
1
reply
160
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 7 weeks ago by 66k • written 7 weeks ago by ▴ 10
2
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13
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725
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
8 weeks ago • updated 7 weeks ago fernanda.backsouza ▴ 10
3
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2
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279
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Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 7 weeks ago by ★ 4.0k • written 8 weeks ago by ▴ 10
2
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2
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275
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
9 weeks ago julia_mcdonough • 0
2
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2
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307
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Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 3 months ago by ★ 4.0k • written 4 months ago by • 0
0
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0
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398
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
7 months ago mch • 0
0
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3
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1.4k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 8 months ago by ▴ 20 • written 9 months ago by • 0
3
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2
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1.2k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 10 months ago by ★ 4.0k • written 10 months ago by ▴ 10
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0
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381
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
11 months ago georgii.vdovin • 0
1
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4
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1.2k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
12 months ago Jiyoung Lee • 0
0
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1
reply
595
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 12 months ago by 42k • written 12 months ago by • 0
0
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5
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1.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
14 months ago • updated 13 months ago ruba-mahmoud • 0
1
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3
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1.2k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 10
0
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13
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5.4k
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KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
15 months ago Laia ▴ 10
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5
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1.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 15 months ago by • 0
4
votes
11
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2.8k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 13 months ago by • 0 • written 15 months ago by ▴ 10
4
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2
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4.7k
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gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 15 months ago by ▴ 50 • written 15 months ago by • 0
1
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7
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2.0k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 15 months ago by ▴ 780 • written 15 months ago by ▴ 10
2
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6
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2.1k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 5 months ago by ★ 4.0k • written 15 months ago by ▴ 10
1
vote
3
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1.2k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 18 months ago by 66k • written 18 months ago by • 0
4
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2
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2.2k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
20 months ago Wuschel ▴ 10
0
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2
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739
views
Shivani
kegg
updated 20 months ago by ▴ 50 • written 20 months ago by • 0
4
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6
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3.8k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 21 months ago by ★ 4.0k • written 24 months ago by ▴ 10
3
votes
13
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2.7k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
22 months ago • updated 16 months ago nute11a ▴ 10
0
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3
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994
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ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
22 months ago abf ▴ 30
1
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1
reply
1.3k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 22 months ago by 66k • written 22 months ago by ▴ 20
0
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2
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903
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How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 22 months ago by ▴ 70 • written 23 months ago by ▴ 20
1
vote
3
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2.0k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 4 months ago by • 0 • written 2.0 years ago by • 0
0
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2
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3.4k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.0 years ago by ★ 3.9k • written 2.0 years ago by • 0
0
votes
1
reply
875
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
0
votes
1
reply
1.3k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.4 years ago by ★ 3.9k • written 2.4 years ago by • 0
0
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0
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848
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Editing KEGG pathways in R
KEGG
2.6 years ago Jordan • 0
1
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0
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1.4k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.6 years ago makrez ▴ 10
1
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0
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1.3k
views
documentation on clusterProfiler output
clusterProfiler KEGG
2.7 years ago rafaela.perez ▴ 10
0
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6
replies
3.9k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.9 years ago Bogdan ▴ 670
0
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2
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1.9k
views
Drawing custom KEGG pathways
pathview KEGG
3.1 years ago • updated 3.0 years ago curiousmind007 ▴ 10
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2
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2.2k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.1 years ago by 66k • written 3.1 years ago by • 0
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0
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1.0k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.2 years ago jol.espinoz ▴ 40
6
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5
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1.6k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.3 years ago by ★ 1.6k • written 3.3 years ago by • 0
2
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2
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1.2k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.5 years ago by 66k • written 3.5 years ago by • 0
0
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3
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1.2k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.0 years ago by 66k • written 4.0 years ago by ▴ 670
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1
reply
1.8k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.2 years ago by 25k • written 4.2 years ago by • 0
2
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2
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1.2k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.2 years ago by 66k • written 4.2 years ago by ▴ 20
0
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0
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812
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.2 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
1.2k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 4.3 years ago by 51k • written 4.7 years ago by ▴ 50
6
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6
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5.2k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.3 years ago by 51k • written 4.3 years ago by ▴ 50
0
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0
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930
views
gage function problem in R
gage R kegg pathview
updated 4.4 years ago by 42k • written 4.4 years ago by • 0
4
votes
4
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1.9k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.6 years ago • updated 4.5 years ago AZ ▴ 30
50 results • Page 1 of 1
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Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
Well, I was looking at the result table (enrich18k@result, or yy@result in your example), and it gives every pathway even the non-significa…
Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Votes
A: dream vignette says limma-voom repeated measures two-group comparison needs two
Answer: Get the latest gene name from Entrez ID
Get the latest gene name from Entrez ID
Answer: biomaRt not working - lazy table error
Answer: How to do DESeq2 on Kallisto Data
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