Showing : KEGG • reset
1
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2.5k
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Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 7 months ago by ▴ 10
0
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4
replies
3.4k
views
Drawing custom KEGG pathways
pathview KEGG
written 4.7 years ago by ▴ 10
0
votes
1
reply
866
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
12 months ago Jessica • 0
0
votes
2
replies
1.1k
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
12 months ago ingrid.h • 0
1
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4
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1.1k
views
pathview - multiple states
pathview Pathways KEGG
14 months ago Philippine • 0
1
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2
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1.1k
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 17 months ago by ▴ 60 • written 17 months ago by • 0
0
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0
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647
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
19 months ago cereyredondo • 0
0
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3
replies
1.3k
views
pathview error
KEGGgraph KEGG
updated 20 months ago by ★ 4.1k • written 21 months ago by • 0
0
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0
replies
557
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
21 months ago danalvoronov ▴ 10
1
vote
1
reply
837
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 21 months ago by 68k • written 21 months ago by ▴ 30
5
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13
replies
4.5k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
22 months ago • updated 21 months ago fernanda.backsouza ▴ 30
4
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2
replies
1.0k
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 22 months ago by ★ 4.1k • written 22 months ago by ▴ 30
2
votes
4
replies
2.7k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 22 months ago by • 0
2
votes
2
replies
821
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 24 months ago by ★ 4.1k • written 24 months ago by • 0
0
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0
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928
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
2.3 years ago mch • 0
0
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4
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4.2k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 16 months ago by • 0 • written 2.4 years ago by • 0
3
votes
2
replies
3.3k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.5 years ago by ★ 4.1k • written 2.5 years ago by ▴ 10
0
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0
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876
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
2.6 years ago georgii.vdovin • 0
1
vote
4
replies
2.4k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.7 years ago • updated 2.6 years ago Jiyoung Lee • 0
0
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1
reply
1.2k
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
votes
5
replies
3.1k
views
enrichKEGG function error
cluster clusterProfiler KEGG
2.8 years ago ruba-mahmoud • 0
1
vote
3
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2.7k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 2.9 years ago by ★ 4.1k • written 2.9 years ago by ▴ 10
0
votes
13
replies
15k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.9 years ago Laia ▴ 10
0
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5
replies
2.4k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.9 years ago by • 0
4
votes
11
replies
5.9k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 2.7 years ago by • 0 • written 2.9 years ago by ▴ 10
4
votes
2
replies
7.5k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 3.0 years ago by ▴ 50 • written 3.0 years ago by • 0
1
vote
7
replies
4.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 2.9 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
2
votes
6
replies
5.5k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 2.1 years ago by ★ 4.1k • written 3.0 years ago by ▴ 10
1
vote
3
replies
2.3k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 3.1 years ago by 68k • written 3.2 years ago by • 0
4
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2
replies
5.6k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
3.3 years ago Wuschel ▴ 10
0
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2
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1.2k
views
Shivani
kegg
updated 3.3 years ago by ▴ 60 • written 3.3 years ago by • 0
4
votes
6
replies
6.3k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 3.4 years ago by ★ 4.1k • written 3.6 years ago by ▴ 10
3
votes
13
replies
4.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.5 years ago • updated 3.0 years ago nute11a ▴ 10
0
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3
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1.7k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
3.5 years ago abf ▴ 30
1
vote
1
reply
2.0k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 20
0
votes
2
replies
1.5k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 3.5 years ago by ▴ 70 • written 3.5 years ago by ▴ 20
1
vote
3
replies
3.4k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 24 months ago by • 0 • written 3.7 years ago by • 0
0
votes
2
replies
4.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
0
votes
1
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1.5k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
votes
1
reply
2.1k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by • 0
0
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0
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1.4k
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Editing KEGG pathways in R
KEGG
4.3 years ago Jordan • 0
1
vote
0
replies
2.2k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
4.3 years ago makrez ▴ 10
1
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0
replies
2.3k
views
documentation on clusterProfiler output
clusterProfiler KEGG
4.4 years ago rafaela.perez ▴ 10
0
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6
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7.5k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
4.5 years ago Bogdan ▴ 670
0
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2
replies
3.0k
views
Can't install KEGGprofile
KEGG RNASeq
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
0
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0
replies
1.7k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
4.9 years ago jol.espinoz ▴ 40
6
votes
5
replies
2.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.9 years ago by ★ 1.6k • written 4.9 years ago by • 0
2
votes
2
replies
1.7k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
3
replies
1.8k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 670
0
votes
1
reply
3.0k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
113 results • Page 1 of 3
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Answer: Subsetting data verses contrasts [DESeq2]? by ATpoint ★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: GSEA in R/Bioconductor course by a2a2haa • 0
Academic researchers often share their breakthroughs and course updates through visual stories, making it essential to have tools that pres…
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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