Showing : KEGG • reset
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KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
5 weeks ago Jessica • 0
0
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2
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549
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
7 weeks ago • updated 5 weeks ago ingrid.h • 0
1
vote
4
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515
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pathview - multiple states
pathview Pathways KEGG
3 months ago Philippine • 0
1
vote
2
replies
466
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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385
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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
876
views
pathview error
KEGGgraph KEGG
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
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0
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323
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
464
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 11 months ago by 68k • written 11 months ago by ▴ 30
5
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13
replies
2.9k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
11 months ago fernanda.backsouza ▴ 30
4
votes
2
replies
647
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 11 months ago by ★ 4.1k • written 11 months ago by ▴ 30
2
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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
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2
replies
575
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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
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0
replies
650
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
16 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
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2.2k
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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601
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
20 months ago georgii.vdovin • 0
1
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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
843
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 21 months ago by 43k • written 22 months ago by • 0
0
votes
5
replies
2.3k
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 23 months ago by ▴ 10
0
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13
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10k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
24 months 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
4.3k
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
3.7k
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 2.2 years ago by 68k • written 2.3 years ago by • 0
4
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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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980
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
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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
2.6 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 2.6 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 2.6 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
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1.1k
views
Editing KEGG pathways in R
KEGG
3.4 years ago Jordan • 0
1
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0
replies
1.9k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
3.4 years ago makrez ▴ 10
1
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0
replies
1.7k
views
documentation on clusterProfiler output
clusterProfiler KEGG
3.5 years ago rafaela.perez ▴ 10
0
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6
replies
5.3k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.6 years ago Bogdan ▴ 670
0
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3
replies
2.6k
views
Drawing custom KEGG pathways
pathview KEGG
written 3.8 years ago by ▴ 10
0
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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
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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
4.0 years ago jol.espinoz ▴ 40
6
votes
5
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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
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1
reply
2.3k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.9 years ago by 25k • written 4.9 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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Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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