Showing : Kegg • reset
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KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
41 minutes ago • updated 10 minutes ago Jessica • 0
0
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1
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203
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
updated 14 days ago by ★ 4.1k • written 14 days ago by • 0
1
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4
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442
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pathview - multiple states
pathview Pathways KEGG
10 weeks ago • updated 9 weeks ago Philippine • 0
1
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2
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404
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Student
metaboliteIDmapping Metabolomics KEGG
updated 4 months ago by ▴ 60 • written 4 months ago by • 0
0
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0
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360
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
7 months ago cereyredondo • 0
0
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3
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772
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pathview error
KEGGgraph KEGG
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
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0
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292
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
9 months ago danalvoronov ▴ 10
1
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1
reply
428
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Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 9 months ago by 68k • written 9 months ago by ▴ 30
5
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13
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2.6k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
9 months ago fernanda.backsouza ▴ 30
4
votes
2
replies
591
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 30
2
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3
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1.1k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 3 months ago by • 0 • written 10 months ago by • 0
2
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2
replies
537
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Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 11 months ago by ★ 4.1k • written 12 months ago by • 0
0
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0
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608
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
15 months ago mch • 0
0
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4
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2.7k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 4 months ago by • 0 • written 17 months ago by • 0
3
votes
2
replies
2.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 18 months ago by ★ 4.1k • written 18 months ago by ▴ 10
0
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0
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576
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
19 months ago georgii.vdovin • 0
1
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4
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1.6k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
20 months ago Jiyoung Lee • 0
0
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1
reply
798
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
5
replies
2.2k
views
enrichKEGG function error
cluster clusterProfiler KEGG
22 months ago • updated 21 months ago ruba-mahmoud • 0
1
vote
3
replies
1.8k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 22 months ago by ★ 4.1k • written 22 months ago by ▴ 10
0
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13
replies
9.1k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
23 months ago Laia ▴ 10
0
votes
5
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1.8k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 23 months ago by • 0
4
votes
11
replies
4.0k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 21 months ago by • 0 • written 23 months ago by ▴ 10
4
votes
2
replies
6.2k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 23 months ago by ▴ 50 • written 23 months ago by • 0
1
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7
replies
2.9k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 23 months ago by ▴ 780 • written 23 months ago by ▴ 10
2
votes
6
replies
3.5k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 13 months ago by ★ 4.1k • written 23 months ago by ▴ 10
1
vote
3
replies
1.6k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 2.1 years ago by 68k • written 2.2 years ago by • 0
4
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2
replies
3.6k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.3 years ago Wuschel ▴ 10
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2
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943
views
Shivani
kegg
updated 2.3 years ago by ▴ 60 • written 2.3 years ago by • 0
4
votes
6
replies
4.8k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.4 years ago by ★ 4.1k • written 2.6 years ago by ▴ 10
3
votes
13
replies
3.3k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.5 years ago • updated 2.0 years 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
1
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1
reply
1.6k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 20
0
votes
2
replies
1.1k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 2.5 years ago by ▴ 70 • written 2.6 years ago by ▴ 20
1
vote
3
replies
2.6k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 12 months ago by • 0 • written 2.7 years ago by • 0
0
votes
2
replies
3.8k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.7 years ago by ★ 4.0k • written 2.7 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 2.8 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
1.6k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3.0 years ago by ★ 4.0k • written 3.0 years ago by • 0
0
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0
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1.0k
views
Editing KEGG pathways in R
KEGG
3.3 years ago Jordan • 0
1
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0
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1.8k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
3.3 years ago makrez ▴ 10
1
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0
replies
1.6k
views
documentation on clusterProfiler output
clusterProfiler KEGG
3.4 years ago rafaela.perez ▴ 10
0
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6
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4.9k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.5 years ago Bogdan ▴ 670
0
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2
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2.5k
views
Drawing custom KEGG pathways
pathview KEGG
3.7 years ago curiousmind007 ▴ 10
0
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2
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2.6k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
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
3.9 years ago jol.espinoz ▴ 40
6
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5
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1.9k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.9 years ago by ★ 1.6k • written 3.9 years ago by • 0
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
3
replies
1.4k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 670
0
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1
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2.3k
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
2
votes
2
replies
1.5k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: KEGG GSEA using Clusterprofiler - ncbi-geneid missing? by Jessica • 0
Nevermind. Just had to change to Uniprot IDs and it worked :)
Comment: GSVA on RNAseq data by Bob ▴ 10
Hi Robert, We were actually very interested in this problem in particular. It seems that using counts for gene sets with varying gene leng…
Comment: plyranges: find exact GRanges match keeping metadata columns by Michael Love 43k
But I will say if you are doing a lot of these, and require exact match, just making it a simple key -- eg `paste0(start,".",end)` -- seems…
Answer: Comparing Mock vs Infected in WT and Knockout Cells by Michael Love 43k
I recommend for questions about statistical analysis plan to meet with a local statistician or someone familiar with linear models in R. I …
Answer: In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowi by ATpoint ★ 4.6k
WGCNA is no Bioconductor package. Consider biostars.org or bioinformatics Reddit, but if you do show a bit more effort please. People appre…
Votes
A: how to extract Granges not overlapping with other ganges?
DESeq2 1.20.0 lfcshrink function
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
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